Patent Publication Number: US-8992833-B2

Title: System and method for multi-analyte detection

Description:
1. RELATED APPLICATIONS 
     This application is a divisional of application Ser. No. 13/094,743, filed Apr. 26, 2011, now U.S. Pat. No. 8,357,537, which is a divisional of application Ser. No. 11/784,596, filed Apr. 6, 2007, now U.S. Pat. No. 7,955,555, which is a continuation of application Ser. No. 10/894,824, filed Jul. 19, 2004, now U.S. Pat. No. 7,220,385, which claims the benefit of U.S. provisional patent application No. 60/489,001, filed Jul. 21, 2003, and 60/488,572, filed Jul. 18, 2003, all of which are incorporated herein by reference in their entireties. 
    
    
     2. BACKGROUND OF THE INVENTION 
     2.1 Field of the Invention 
     Generally, the present invention relates to a system and method for multiple analyte detection. More particularly, multiple analytes are contained within a single sample and analyzed simultaneously using high-speed digital signal processing. 
     2.2 Description of Related Art 
     Disease analysis, research, and drug development depend heavily on laboratory assay analysis. An example of an assay that has become commonplace in today&#39;s laboratory is the immunoassay. Many other types of laboratory analyses are also conducted in today&#39;s laboratories, such as analysis on blood, urine, serum, blood plasma, and other body fluids for proteins, viruses, bacteria, and other conditions. 
     Traditionally, laboratory assay analyses were very time consuming processes, requiring lab personnel to perform precise measurements of reagents and samples, mixtures, centrifuging, etc. Each step of these analyses typically needs to be repeated multiple times to acquire statistically significant data. Furthermore, the processes are often wasteful of costly solvents, solutions, reagents, require numerous man-hours, and are generally slow. 
     Accordingly, automated devices were envisioned and developed to quicken the process, generate more accurate results and make the process more economical and efficient. However, a drawback of these devices is that a limited number of analyses can be run on any given sample at any time. Therefore, much time is still required to analyze a sample for multiple analytes. 
     Accordingly, a system and method for testing multiple analytes, with little or no human intervention, from a single test sample would be highly desirable. 
     3. BRIEF SUMMARY OF THE INVENTION 
     According to one embodiment, a system and method is provided for the simultaneous detection of multiple analytes. The system comprises a housing and a reagent carousel rotatably coupled to the housing. Also rotatably coupled with the housing is an incubator carousel. Magnetic material is associated with the incubation carousel for assisting in washing samples held by the incubator carousel. Furthermore, at least one robot is coupled to the housing. The robot is configured to manipulate the reagent carousel and/or the incubator carousel. Reaction vessel handlers are responsible for moving reaction vessels between locations, such as a pre-testing location, testing location, and post-testing location. There is also at least one laser based detector for analyzing samples following mixing the sample with reagents. 
     In a preferred embodiment, there is a flow cytometer for conducting the analysis of the samples. It is also preferred that washers are included for washing the robots and robot probes. 
     According to another embodiment the incubator carousel further includes a plurality of rings. Each ring is rotatable with respect to the other rings such that high throughput is achieved from the system. 
     According to yet another embodiment, the reagent carousel is configured to contain reagent kits. The reagent kits are accessible by at least one robot. The kits and reagent carousel are designed to be utilized during use of the system and without interruption of overall system processes. 
    
    
     
       4. BRIEF DESCRIPTION OF THE DRAWINGS 
       For a better understanding of the nature and objects of the invention, reference should be made to the following detailed description, taken in conjunction with the accompanying drawings, in which: 
         FIG. 1  is a block diagram showing general features of a multi-analyte detection (“MAD”) system according to an embodiment of the present invention; 
         FIG. 2  is an perspective view of a MAD system according to an embodiment of the present invention, partially disassembled to show component modules and subsystems; 
         FIG. 3  is a top schematic view of the MAD system of  FIG. 2 ; 
         FIG. 4  shows typical flow cytometer fluidics as incorporated in an embodiment of the present invention; 
         FIG. 5  shows a flow cuvette design and wavelengths of two laser beams according to an embodiment of the present invention; 
         FIG. 6  shows an optics design according to an embodiment of the present invention; 
         FIG. 7  shows a bead “map” showing relative fluorescence signals from two classifier dyes for a set of 25 beads according to an embodiment of the present invention; and 
         FIG. 8  shows washing of magnetic beads using electromagnets according to an embodiment of the present invention; 
         FIG. 9  is a perspective view of a sample rack handler assembly according to an embodiment of the present invention; 
         FIG. 10  is a block diagram of the specimen rack handler assembly of  FIG. 9 ; 
         FIG. 11  is a perspective view of a reaction vessel (“RV”) handler and supply assembly according to an embodiment of the present invention; 
         FIG. 12  is a perspective view of a reaction vessel supply sub-assembly of  FIG. 11 ; 
         FIGS. 13A-C  depict a RV detection mechanism for use in the RV supply assembly of  FIG. 12 ; 
         FIG. 14  is an illustration of operation of RV the supply assembly of  FIG. 12 ; 
         FIG. 15  is a block diagram of an RV supply assembly according to the present invention; 
         FIG. 16  is an illustration of a reaction vessel handler assembly according to an embodiment of the present invention; 
         FIGS. 17 ,  18 ,  19 A and  19 B are detailed illustrations of a reaction vessel handler and related components; 
         FIG. 20  is a block diagram depicting an RV handler assembly; 
         FIG. 21  shows a reaction vessel according to an embodiment of the present invention; 
         FIG. 22  is a perspective view of a sample handler assembly according to an embodiment of the present invention; 
         FIG. 23  is a cross-sectional view of a sample aspiration probe and clean station according to an embodiment of the present invention; 
         FIG. 24  is a block diagram depicting a sample handler robot; 
         FIGS. 25 and 26  are perspective view of a reagent storage assembly according to an embodiment of the present invention. 
         FIGS. 27A and 27B  are cross-sectional perspective views of the reagent storage assembly of  FIG. 25 ; 
         FIGS. 28A-C  show a reagent pack and bottles according to an embodiment of the present invention; 
         FIGS. 29A-C  show a reagent pack piercer according to an embodiment of the present invention; 
         FIG. 30  shows a reagent storage assembly clutch mechanism according to an embodiment of the present invention; 
         FIGS. 31A-C  are cross-sectional side views showing operation of the pack piercer of  FIGS. 29A-C ; 
         FIG. 32 . is a perspective view of a reagent pack lid opener according to an embodiment of the present invention; 
         FIG. 33  is a perspective view of a reagent robot assembly according to an embodiment of the present invention; 
         FIG. 34  is a top view of the reagent robot of  FIG. 33 , showing a range of movement; 
         FIG. 35  is a block diagram of the reagent robot assembly of  FIG. 33 ; 
         FIG. 36  is an exploded perspective view of an incubator and separation carousel assembly according to an embodiment of the present invention; 
         FIG. 37  is a block diagram of the incubator and separation carousel assembly of  FIG. 36 ; 
         FIG. 38  is an illustration depicting a separation mechanism employed in an embodiment of the incubator and separation carousel assembly of  FIG. 36 ; 
         FIG. 39  is a perspective view of a partially assembled incubator and separation carousel assembly of  FIG. 36 ; 
         FIG. 40  shows a wash station according to an embodiment of the present invention; 
         FIG. 41  is a block diagram of a wash station according to an embodiment of the present invention; 
         FIG. 42  is a perspective view of a detector transfer robot assembly according to an embodiment of the present invention; 
         FIG. 43  is a block diagram depicting the detector transfer robot; 
         FIGS. 44A and 44B  depict a reaction vessel waste assembly according to an embodiment of the present invention; 
         FIG. 45  is a close up perspective view of the MAD system of  FIG. 2 , showing containers and other components of a fluidics system; 
         FIGS. 46A and 46B  are block diagrams of a fluidics system according to the present invention; 
         FIGS. 47A and 47B  are detailed schematic diagrams of a fluidics system according to the present invention; 
         FIGS. 48A and 48B  are illustrations of different embodiments of fluid reservoirs with liquid level sensors; 
         FIGS. 49-51  are flow charts depicting an example of a method of use of a MAD system for performing a serology IgG assay panel; and 
         FIG. 52  is a detailed functional block diagram of a MAD system according to the present invention. 
     
    
    
     Like reference numerals refer to corresponding parts throughout the several views of the drawings. 
     5. DETAILED DESCRIPTION OF THE INVENTION 
     5.1 Overview of the Multi-Analyte Detection (“MAD”) System 
     A general overview of the technology employed in the system follows. It should be appreciated by one of ordinary skill in the art that the following description of the technology employed in the system is intended as exemplary and educational and is not intended to limit the invention. Furthermore, any numerical values, ranges, materials, temperatures, times, or the like, given below are preferred values, not intended to limit the present invention. Following the general description is a more detailed description of each of the modules and various sub-modules and other components. 
     Referring to  FIG. 1 , the multi-analyte detection system  10  (also referred to herein as MAD system  10 ) includes a detector module (“DM”)  20 , a sample processing module (“SPM”)  30 , and a host computer  40 . Each of these modules  20 ,  30 ,  40  includes assemblies, sub-assemblies, and/or components that perform various tasks within the overall system and method of using the MAD. (Note that the terms “assembly” and “sub-assembly” are used throughout to help identify levels of component systems within overall system  10 , however such term are not meant to limit the invention and may be used interchangeably.) 
     For example, sample processing module  30  includes assemblies for specimen handling 31, reagent storage  32 , incubation and assay processing  33 , control of on-board assemblies and processes  34 , storage and delivery of fluids and storage of wastes  35 , cleaning and maintenance functions  36 , and for communication  36  between and among the various assemblies and modules. Detector module  20  includes an analyzer  22  for analyzing samples processed by SPM  30  and interfaces for communicating with other modules and assemblies and for sending assay data to host  40 . 
     Host computer system  40  is generally responsible for providing oversight of necessary operations from instrument control to results evaluation, data storage, quality control, mainframe bidirectional interfacing, and operator assistance. Specific instrument control activities include movement of samples, pipetting samples, pipetting reagents, flushing samples, analyzing samples, reporting data, and troubleshooting the device. 
     Host computer  40  preferably includes a processor  41 , or central processing unit (CPU)  41 , memory  45 , interfaces  42  for communicating with modules  20 ,  30 , other communication circuitry  45 , and a user interface  44  that can include, e.g., a monitor, a keyboard, a trackball, or mouse, and/or a touch screen for data entry. Host computer system  40  also preferably, although not necessarily, includes a printer or other peripheral output devices. Memory  45  includes software and data for performing various operations and control of system  10 . For example, memory  45  typically includes software modules such as: an operating system  45 - 1 ; one or more assembly control modules  45 - 2  including instructions for operation and control of modules  20 ,  30  and other subsystems and components of system  10 ; assay protocols  45 - 3 ; analyzing, processing and storing data  45 - 4 ; quality control  45 - 5 ; an expert system  45 - 6  and a instructions and data related to scheduling  45 - 7  of assays and procedures. 
     Referring to  FIG. 2 , a preferred embodiment of MAD system  10  is a self contained, fully automated random assay system incorporating a sample processing module  30  having a number of automated assemblies and components for processing samples and a detector module  20  for analyzing the samples. 
     MAD system  10  is capable of multiplexing a number of assays in the same reaction tube and preferably employs a multiplexed bead-based chemistry system for performing numerous assays. For example, in one embodiment, system  10  is capable of performing up to 25 or more individual assays, in another embodiment up to 100 individual assays, and in yet another embodiment more than 100 individual assays simultaneously in a single reaction vessel. 
     Generally, detector module  20  utilizes an advanced analyzer to detect the presence of analytes, such as antigens, antibodies receptors, peptides, oligonucleotides, DNA, RNA, small molecules, viruses, viroids, cells, and the like, in patient samples by integrating the technologies of fluoroimmunoassay and flow cytometry. This combination of advanced technologies allows system  10  to perform, e.g., at least 200 measurements per analyte per specimen, and about 100,000 measurements per minute, yielding up to about 2,200 results per hour. Detector module  20  incorporates a flow cytometer that detects labeled microspheres or beads in a sample, and communicates with hardware and software in host computer  40  for assay control and data analysis. Optionally, detector module  20  incorporates its own computer processor and memory for providing some level of control and analysis and communicating with host  40 . 
     In a preferred embodiment a flow cytometer of detector module  20  analyzes individual microspheres by size and fluorescence, distinguishing preferably three fluorescent colors, green (550-610 nm emission), orange (585-650 nm emission), and red (&gt;650 nm emission), simultaneously. Microsphere size, determined by 90-degree light scatter, is used to eliminate microsphere aggregates from the analysis. Orange and red fluorescence are used for microsphere classification, and green fluorescence is used for quantification of analyte. Additional details and examples of detector module  20  are described in section 5.2 below. 
     Major assemblies and components of sample processing module  30  include a specimen rack handler assembly  50 , a reaction vessel handler assembly  52 , a reaction vessel supply system  54 , an incubator and separation carousel  56 , a reagent storage assembly  58 , a reagent robot  60 , a wash robot  62 , a solid waste system  64 , a sample handler  66 , and a fluidics system  68 . Each of these components are shown in  FIG. 3  and described in more detail in section 5.3 below. 
     5.2 Detector Module 
     5.2.1 Overview of Detector Module (“DM”) 
     According to a preferred embodiment, detector module  20  is a dual-laser flow cytometer system including fluidic, electronic and optical subassemblies. The main optical components of the detector module are: red laser for bead classification, green laser for label excitation, a PMT (photomultiplier tube) for detecting label emissions and photodiodes to detect signal coming as a result of excitation of the classification dyes in microparticles. 
     More particularly, in one embodiment detector module  20  is an advanced immunoassay analyzer incorporating SUSPENSION ARRAY (LUMINEX CORPORATION). Briefly, SUSPENSION ARRAY analysis involves the process of analyzing populations of microspheres (or “beads”) having unique intensities of red and near infrared dyes, allowing each bead population to be identified and analyzed separately. Bead populations are distinguished with unique binding molecules making each population sensitive to a particular analyte. A fluorescent indicator dye is then used to quantify the amount of bound analyte on each bead. Calibrators convert average population intensity into analyte concentration. Performing the chemistry on microspheres, e.g., on the surface of microspheres, leads to significant reduction in reagents, yielding significantly lower costs for consumables. Additional details may be found in U.S. Pat. Nos. 6,592,822; 6,528,165; 6,524,793; 6,514,295; 6,449,562; 6,411,904; 6,366,354; 6,268,222; 6,139,800; 6,057,107; 6,046,807; 5,981,180; 5,802,327; and 5,736,330; as well as in published U.S. Application Numbers 20030132538, and 20020182609, each of which in incorporated by reference herein in its entirety. 
     Detector module  20 , in one embodiment, includes a flow cytometer having one or more lasers, optics, photodiodes, a photomultiplier tube, and digital signal processing to perform simultaneous, discrete measurements of fluorescent microspheres. In one embodiment, three avalanche photodiodes and a high sensitivity photomultiplier tube (PMT) receive photon signals from the microspheres. Detector module  20  in this example digitizes the waveforms and delivers the signals to a digital signal processor (DSP). The detector module works with the SPM and host computer to perform multiplexed analysis simultaneously by using the flow cytometer and digital signal processor to perform real-time analysis of multiple microsphere-based assays. Because a flow cytometer has the ability to discriminate different particles on the basis of size and/or fluorescence emission color, multiplexed analysis with different microsphere populations is possible. Differential dyeing microspheres, emitting light at two different wavelengths, allows aggregates to be distinguished and permits discrimination of, in one embodiment, up to about 25 different sets of microspheres, in another embodiment up to about 100 different sets of microspheres, and in yet another embodiment more than 100 different sets of microspheres. Several control beads are used in every analysis to ensure quality control of the results. The system can analyze small-molecular weight (e.g., T4) and large molecular weight analytes including, for example, IgG, IgA, and IgM antibodies, and glycoprotein hormones. 
     In one embodiment, fluorescence excitation a preferred embodiment of a MAD system involves two solid state lasers. These lasers illuminate the microspheres as they flow single file through the cuvette. The fluorescent signals are discriminated with selective emission filters and are converted into intensity units by using the DSP. There are two different fluorophores present within the microbeads which emit with two different emission profiles that are separately measured in order to define the address (test analysis) of the bead. 
     Immunochemical reactants, such as antigens, antibodies receptors, peptides, oligonucleotides, DNA, RNA, small molecules, viruses, viroids, cells, and the like of these assays become bound to the surfaces of uniquely addressed fluorescent microscopic beads. The fluorescent spectral address of each bead identifies each of the assays performed simultaneously on a single sample. Based on its fluorescent signature, every microsphere is classified to its own unique region. In addition, each bead is scanned for the presence of a reporter fluorescence that quantifies the bead-assigned assay at the bead surface. The MAD microspheres are highly uniform, polystyrene-based particles that have been crosslinked during polymerization to provide physical strength and stability. They also contain a magnetic core so that they can be attracted to an electromagnet to facilitate facile washing. The beads may be magnetic, paramagnetic, superparamagnetic or the like to facilitate processing and washing of samples. Varying ratios of different fluorochromes embedded within each microsphere give each bead a unique spectral address. Each microsphere is dyed to emit light in a certain classification channel. All microspheres of given emissions represent a distinct assay within a multiplex of assays. A reporter channel is used to detect fluorescence bound to the surface of each microsphere, and each reporter emission quantitates each of the distinct assays. Only one reporter is needed for a multiplex of assays. To ensure the stability of this address, the microspheres should be protected from light and high temperatures. 
     One technology employed in the MAD system is flow cytometry. Flow cytometry is a technique that simultaneously measures and then analyzes multiple physical characteristics of single particles, usually cells, as they flow in a fluid stream through a beam of light, most commonly from a laser. As a technique, flow cytometry is somewhat analogous to fluorescent microscopy; one major difference is that flow cytometry provides a digital result. In flow cytometry, measurements are performed on particles (e.g., cells or microbeads) in liquid suspension, which flow one at a time through a focused light (e.g., laser) beam at rates up to several thousand particles per sec. 
     The properties measured by flow cytometry may include a particle&#39;s relative size, relative granularity, internal complexity, and relative fluorescence intensity. These characteristics are determined using an optical-to-electronic coupling system that records how the cells or beads scatter incident light and emit fluorescence. 
     The detector module flow cytometer includes three main systems—detector fluidics, optics, and electronics. The detector fluidics system transports particles in a stream to a laser beam for interrogation. A diagram of a typical flow cytometer fluidics system is shown in  FIG. 4 . Details of the MAD flow cuvette design and the wavelengths of the two laser beams used in MAD system are provided in  FIG. 5 . The optics system consists of lasers to illuminate the particles in the sample stream and optical filters to direct the resulting light signals to the appropriate detectors. Details of the MAD detector optics design are provided in  FIG. 6 . The electronics system converts the detected light signals into electronic signals that can be processed by the computer  40 . 
     As shown in  FIG. 4 , in the MAD flow cytometer  100 , particles  102  are carried to the laser intercept  104  in a fluid stream; this liquid is referred to as sheath fluid  106 . Particles  102  are carried by a microscopic jet of buffer and are hydrodynamically focused in the center of the fast moving stream  106  of the sheath fluid. The particles  102  pass one by one (some particles in the flow stream may not be individual entities; particles may be bound to each other or in such close proximity that they are detected as a single bead) through an intense beam of excitation light in the measuring region of the flow cytometer. Each particle thereby produces short flashes of fluorescence, the intensities of which are proportional to the content of the fluorescently labeled constituent.  FIG. 4  shows a flow cytometry fluidics system according to an embodiment of the present invention showing the flow direction, injector tip  108 , flow cell  110 , laser beam  104 , and sheath fluid  106 . 
     The fluorochromes emit fluorescent light many times during the transit time of a bead through the flow cuvette. 
     Suspended particles or cells preferably from about 0.2 to about 150 micrometers in size are suitable for flow cytometric analysis. The portion of the fluid stream where particles are located is called the sample core. When particles pass through the laser intercept, they scatter laser light without loss or gain of energy. Any light excited molecules present on the particle fluoresce. The scattered and fluorescent light are collected by appropriately positioned lenses. A combination of beam splitters and filters directs the scattered and fluorescent light to the appropriate detectors. The detectors produce electronic signals proportional to the optical signals striking them. 
     List mode data (photon recordings are recorded in a list) are collected for each particle or event. The characteristics or parameters of each event are based on light scattering and fluorescent properties. The data are collected and stored in a computer. These data can later be analyzed to provide information about subpopulations within the sample. 
       FIG. 5  details a MAD flow cytometry cuvette flow cell  110  according to an embodiment of the present invention showing the cell dimensions and the laser beam wavelengths  114 ,  116 . The dimensions shown, e.g., approximately 200 μm×200 μm, are approximate inner dimensions of a suitable flow cuvette. According to one embodiment, the outer dimensions are preferably about 2.2 mm by 2.2 mm. One skilled in the art will appreciate that cuvettes of other dimensions or characteristics are known and may be used without departing from the scope of the invention. 
       FIG. 6  details a MAD optics design according to an embodiment of the present invention showing flow cell  110 , reflectors  124 , 126 , lasers  116 , 114 , lenses  120 ,  122 , and detectors  128 , 130 . 
     In a preferred embodiment, detector module  20  is equipped with two lasers  114  and  116 . Particular characteristics of lasers  114  and  116  are described below, however one skilled in the art will appreciate that numerous other laser systems and analyzers are known in the art and may be used depending upon the types of assays one desires to perform; any such lasers or alternative analyzers or detector modules may be employed in detector module as part of the overall MAD system without departing from the scope of the present invention. 
     In this example, diode laser  116  produces about 7 mWatts of about 635 nm (red) light. This laser is also referred to herein as red laser  116  or the classifier laser  116  since it is used to excite the classifier dyes within a bead leading to the identification of the bead region to which the bead belongs. 
     The second laser, laser  114 , is preferably a diode-pumped, solid state, continuous wave (CW), doubled Nd:YAG laser. In this example embodiment, laser  114  produces about 15 mWatts of power and about 532 nm (green) light. Laser  114  is also referred to herein as green laser  114  or reporter laser  114  since it functions to excite the reporter (label) groups at the microsphere or bead surface. Green laser  114  preferably has a power stability of less than +/−2% over 8 hours, and a beam diameter of 0.32 mm+/−10%. Laser  114  uses yttrium aluminum garnet (YAG) as the matrix material, doped with neodymium (Nd:YAG). A 15 mm lens is used as the primary focusing lens for the 532 nm laser  114 . 
     Further, in this embodiment, there are two 4 mm lens assemblies  120 ,  122  located approximately 900 mm from the laser beam path. They are precision aligned to the cuvette and collect the fluorescent signals, both reporter and classifier. A 550 nm-610 nm reflector is used to deflect the reporter signal to the single photomultiplier in the MAD system. A 630 nm-760 nm reflector is used to deflect the classifier signal to two classification channel avalanche photodiodes. One photodiode detects the “red’ classifier dye emission and the other the “orange” classifier dye emission. Orthogonal scattered light (from the beads) is also measured on the system using a third avalanche photodiode. A block, referred to as the “U” block, houses the classifier and doublet discriminator lenses, the diodes, and circuitry. In one embodiment, the flow cuvette is made of quartz and has a width and depth of 200 μm. The light gathered by the photodetectors initially exits through one of the cuvette&#39;s walls, is reflected by a mirror, and finally passes through a filter before reaching the detector. The numerical aperture of the detector is 0.62. The mirror causes about 2% loss in light intensity and the filter cuts the intensity by about 50%. Fluorescence emission from the bead surface takes place at all angles and only a few percent of the total emitted photons are collected by the first mirror due to the physical limitations of the optics design. Therefore, only a very small percentage (e.g., probably &lt;1%) of emitted photons are actually recorded by the detector. 
     Alternatively, other more powerful 532 nm lasers  114  may be used to improve the analytical sensitivity of immunoassays. In particular, an approximately 50 mWatt laser photobleaches the primary detector molecule, B-phycoerythrin, used as a reporter for most assays. The optimal wattage for 532 laser  114  is about 10-20 mWatt in this example, however other wattages or lasers may be used. 
     There are two fluidic paths in this MAD system detector module. The first path involves a syringe driven mechanism that controls the small volume sample uptake. This syringe driven system transports a user specified volume of sample from a sample container to the reaction vessel (RV). After reaction incubation(s), the sample is injected into the flow cuvette at a steady rate for analysis. Following analysis, the sample path is automatically purged with sheath buffer by the second fluidics path. This process effectively removes residual sample within the tubing, valves, and probe. The second fluidics path is driven under positive air pressure and supplies the sheath fluid to the cuvette. 
     As will be described in more detail below, in this embodiment, following the last aspiration of wash, MAD system  10  dispenses wash buffer, e.g., approximately 20-70 μA, more preferably about 50 μl, into the reaction vessel (RV) in preparation for fluorescence reading. Approximately all of this volume is aspirated to the detector. The first approximately 5 μl is ignored by the detector before reading commences. The length of time to read the beads is generally dependent on the bead concentration since in this example there is a defined number of beads read for all regions, e.g., in this example about 200 beads read for all bead regions. This typically requires from about 5 to 25 sec. Counting of beads on the MAD system  10  terminates when either the defined number of each regional bead in the assay panel are counted, or when the allocated time for fluorescence analysis is completed. Since not all beads are at exactly the same concentration, most bead sets will acquire more than 200 counts. Analysis terminates with the last bead region to reach the defined number, e.g., 200, counts. The allocated time is determined by the sample flow rate and by its volume. The assay cycle time for the preferred timing sequence used by the IgG and IgM serology panels, and the systemic autoimmune panel, is, e.g., 30-40 sec, more preferably about 36 sec. The percent of the cycle time that the MAD system is reading fluorescent beads with the preferred timing sequence is therefore in this particular example about 28% to 53%. Of course, other time cycles may apply depending upon system set-up and types of assays performed. 
     The transit time for an individual bead to travel from the flow cuvette  110  location in which it is interrogated by red laser  116  to the location where the bead is illuminated by green laser  114  is about 35 μsec. The instrument&#39;s firmware measures the exact transit time during the detection calibration step. In an actual assay, the detector measures this time from bead&#39;s coincident CL1 and CL2 readings (see  FIG. 7 ), and then measures the conjugate derived fluorescence (RP-1) (see  FIG. 7 ). Since the flow rate is approximately constant, MAD system  10  “knows” that a given green fluorescent signal is associated with the red and orange emissions registered 35 μsec earlier. Because the bead concentration in the flow stream is low, there is only a very low statistical chance that the RP-1 signal would be misassigned to the wrong bead, i.e., a close proximity second bead in the flow cell. Since the flow rate for the MAD system is nominally 2.3 msec, a bead would flow 81 microns in 35 μsec. The distance between the focal points for the two lasers  114 ,  116  is therefore about 81 microns. 
     Because the fluorescence readings of the red  116  and green  116  emissions must be temporally coordinated, it is desirable that the flow rate remain constant within a narrow range. Some change in flow rate does occur and the MAD system can accommodate minor fluctuations. Larger changes in the flow rate of beads through the detector would cause significant problems. When detector module  20  of instrument  10  is calibrated, not only are the voltage settings adjusted to attain the three pre-designated RFI readings, but the instrument also adjusts for the time required for bead transit from the red  116  to the green  114  laser illuminations. As the flow rate changes due to pressure changes in the system, the transit time changes in a near linear relationship. Once MAD system  10  is calibrated and the transit time established, subsequent change in pressure (and thus flow rate) will affect the results, leading to deleterious effects including lower RFI values and decreased precision. 
     In one embodiment, detector module  20  takes somewhat less time to read the beads than the LUMINEX LX100, all else being equal. This is because the MAD system&#39;s analyzer preferably employs efficient magnets for wash and separation of analytes. Fewer beads are therefore lost with the MAD system  10 , the concentration of beads in the flow cell is higher, and the time to count  200  beads per region is less. 
     Fluorescent measurements of beads on detector module  20  are gated, where a gate is a boundary that defines a subset or sub-population of events. Gates are set by electronically drawing boundaries around the data subsets. Gates can be used either for data acquisition or analysis. Inclusive gates select only the events that fall within (and on) the boundary. Exclusive gates select only the events that fall outside of the boundary. (The gates described in this paragraph are data acquisition and exclusive gates). One gate is fixed by the firmware and two gates are optionally set by the operator. The first gate is automatically established and determines whether the CL1 and CL2 signals for an individual bead fit within one of the established bead map regions. If it does, the bead passes that gate. If not, the data for the bead is filtered out and subsequently ignored. The second gate, which is operator established through the user interface, is the doublet discriminator gate. This gate is based on the light scatter measurement of the bead. The purpose of this gate is to exclude bead aggregate events (larger than an individual bead) or bead debris events (smaller than an individual bead). The third filter is the RP-1 gate. This gate excludes two types of events—zero RFI beads and very bright beads (high statistical outliers) from further data analysis. The last gate is also user defined. 
     Fluorescent spillover occurs when two or more emission spectra overlap so that selective filtering cannot occur. In some flow analyzers, emission spillover is corrected using a technique called compensation. Compensation involves subtraction of some emission percentage from another emission signal. One embodiment of system  10  does not use compensation; however, the reporter signal does not significantly spill over into the classification emission. 
     The reporter fluorochrome is bound to the surface of the microsphere and provides raw analytical data. Because a microsphere suspension provides near liquid phase reaction kinetics, each microsphere of a particular spectral address theoretically binds an equal number of reporter molecules. Equal binding results in a statistically even distribution of reporter on each microsphere in a set. This means numerous replicates for each microsphere population are measured from a single well. The confidence in a given measurement strengthens with increased replicate measurements. For adequate confidence, 200 events per microsphere set in each well is usually sufficient. 
     5.2.1 Characteristics and Uses of Microspheres 
     In a preferred embodiment of system  10 , instead of employing commonly used microtiter wells to host the immunochemistry-based assays, the immunoassay reactions occur on the surface of microscopic, magnetic, polystyrene-core beads known as microspheres. Suitable microspheres are disclosed, for example in the LUMINEX patents listed above. Although such microspheres are not necessarily part of detector module  20 , they are described herein as they are integral to the principals of operation of an exemplary embodiment of the detector module  10  as described. 
     Prior to use, microspheres are maintained in suspension in a bead reagent solution. Individually dyed with combinations of two different fluorescent dyes (red and orange), a microsphere may have one of many possible levels of classifier dye fluorescent intensities. The various combinations of dyes create a sets of, in one embodiment, up to 25 uniquely color-coded microsphere sets, in another embodiment up to 100 uniquely color-coded microsphere sets, and in yet another embodiment more than 100 uniquely color-coded microsphere sets. In one embodiment, antigens or antibodies indicative of a specific bacterial or viral antigen, protein, or other molecule are coated onto the surfaces of each uniquely color-coded bead set, making each different microsphere set representative of a different assay. 
     Because in this example each microsphere is coated with antigens or antibodies specific for a given condition, each microsphere is equivalent to an individual microtiter well used in many enzyme-linked immunosorbent immunoassays (ELISAs). Alternatively, beads may be coated with proteins, antibodies, ligands or the like in order to run a wide variety of assays and assay formats. MAD system  10  can simultaneously run (multiplex), according to one embodiment, up to 25 assays in a single reaction vessel, in another embodiment up to 100 assays in a single reaction vessel, and in yet another embodiment, more than 100 assays in a single reaction vessel, using as little as 5 μl of sample. Beads may include fluorescent or other labels, or may be secondarily labeled during processing with labeled antibodies that bind to a target molecule after it is bound to a bead. 
       FIG. 7  shows microspheres serving as the vehicle for molecular reactions. The microspheres are approximately 8.0 μm polystyrene microspheres that bear carboxylate functional groups on the surface. The microspheres are available in 25 distinct sets  134  that are classified by the flow cytometer by virtue of the unique orange/red emission profile of each set, as shown in  FIG. 7 . Microspheres of this size provide sufficient surface area for covalent coupling of 1-2×10 6  target molecules per microsphere. In use, fluorescence classification of dual-labeled fluorescent microspheres is used. Two-dimensional dot plots report the classification of a 25 microsphere set based on simultaneous analysis of logarithmic orange fluorescence (FL2) and logarithmic red fluorescence (FL3).  FIG. 7  also shows the positioning of each numbered bead set with regions  6  (labeled “ 134 - 6 ”) and  100  (labeled  134 - 100 ) containing the least and most amount, respectively, of combined orange and red dyes. 
     Fluorescent reactants, e.g., fluorescent antibodies, antigens, or nucleic acid probes provide specific signals for each reaction in a multiplexed assay. Because each fluorescent reactant binds specifically to a target that is present on only one bead set in a multiplexed assay, the soluble reactants do not need to be differentially labeled. All fluorescent molecules are labeled with a fluorophore such as the organic green-emitting dyes BODIPY and fluorescein isothiocyanate, or a more commonly used biological fluorophore such as phycoerythrin. Any fluorochrome can be used as a reporter; however, each fluorochrome has a characteristic emission spectrum which affects the amount of spillover into the orange fluorescence channel. In one example green-emitting fluorophores are used. 
     To prepare a multiplexed assay, individual sets of microspheres are conjugated with the target molecules required for each reaction. Target molecules may be antigens, antibodies, oligonucleotides, receptors, peptides, etc. Fluorescent reactants may be complementary oligonucleotides, antigens, antibodies, receptors, etc., i.e., any molecule that will specifically bind to the target molecule. After optimizing the parameters of each assay separately in a nonmultiplexed format, the assays can be multiplexed by simply mixing the different sets of microspheres. The fluorescent reactants also are mixed to form a cocktail for the multiplexed reactions. The microspheres are then reacted with a mixture of analytes, for example in a biological sample, followed by the cocktail of fluorescent reactants. After a short incubation period, the mixture of microspheres, now containing various amounts of fluorescence on their surfaces, are analyzed with the flow cytometer. Data acquisition, analysis, and reporting are performed in real time on all microsphere sets included in the multiplex. As each microsphere is analyzed by the flow cytometer, the microsphere is classified into its distinct set on the basis of orange and red fluorescence, and the green fluorescence value is recorded. Two hundred individual microspheres of each set are analyzed and the median value of the green fluorescence is reported. 
     With respect to protein antigens, methods for coupling proteins to bead surfaces are well known. For example, covalent coupling of protein antigens to bead surface carboxyl groups by amide bond formation requires protonated carboxylic acids for the initial activation and esterification steps of the conjugation reactions. Since the pKa of carboxylic acids is higher in ethanol than in water, conducting the initial steps in buffered ethanol is advantageous compared to conducting them in aqueous buffer. For example, ethanol raises the pKa of methacrylic acid from pH 4.9 to approximately pH 6.0, which means that approximately ten-fold more carboxyl groups will be available for coupling when the beads are activated and esterified at pH 5.0 in buffered ethanol compared to pH 5.0 in aqueous buffer. However, because the classification dyes used to define the spectral addresses of the beads are soluble in organic solvents and are only infused into the bead surface, it seemed possible that exposure of the beads to ethanol would result in leeching of these dyes. Depending on the extent of extraction, leeching of classification dyes could reduce classification efficiency, and if extreme, could even cause misclassification. Other potential effects of ethanol include increasing bead autofluorescence and decreasing bead dispersion in aqueous solution. The objective of a conducted experiment described below was therefore to determine whether exposure of dyed beads to ethanol compromised classification efficiency, increased autofluorescence, and/or decreased dispersion in aqueous solution. To address these issues, dyed beads were exposed to absolute ethanol for four hours and sampled at 30 minute intervals. At the end of the exposure period, the beads were evaluated sequentially in an LX-100 flow fluorometer and classification, autofluorescence, and bead dispersion data were acquired. The data showed no change in classification efficiency and bead dispersion for the duration of the study, however, there was a nominal increase in autofluorescence for some regions after 120 minutes and a substantial increase for these regions after four hours. Overall, the data from these experiments indicated that activation and esterification of bead surface carboxyl groups for 60 minutes in 90% ethanol would not have adverse effects on the classification efficiency, autofluorescence, and dispersion of dyed beads. A consequence of this could be rearrangement of the bead surface ultrastructure through redistribution of hydrophilic and hydrophobic polymers, and a change in the ability of the beads to remain dispersed in aqueous solution. This concern could be dismissed however, because doublet discriminator data did not reveal any impact of ethanol on bead dispersion. 
     The data from this study indicated that exposure of dyed beads to ethanol for 60 minutes during carboxyl activation and esterification would not have any consequence on classification efficiency, autofluorescence, or dispersion of the beads in aqueous solution. Thus, exploiting the power of ethanol to raise the pKa of bead surface carboxylic acids offers a practical opportunity to increase the coupling efficiency of bead ligation procedures. 
     An embodiment of detector  20  uses a 14-bit analog to digital converter (ADC). The resolution in terms of histogram bin width is about 1/32,000. This is fairly limited resolution. A current version of the DSP in the LUMINEX obtains eight fluorescent readings from each bead during its lifetime in the focused region of the reporter laser. The RFI values reported by the DSP of the detector are essentially an integration of the eight fluorescent readings per bead. The height (direction of flow) of the laser-illuminated region in the detector flow cell is about 30 μm and the velocity of the sample stream is roughly 2.3 msec. Thus, the residence time of the bead in the illuminated region is about 13 μsec. Assuming a fluorescence lifetime of 5 nsec for the reporter label, the beads could be excited and then fluoresce 2,600 times (13 μsec/5 nsec) during the transit time (assuming no photobleaching). Therefore, reporter emission is recorded for less than 1% of the time the bead-bound label is in the laser light path. 
     In one embodiment, detector module  20  is a flow cytometer that uses a two-step calibration initiation. One calibrator (CAL-1) adjusts the correct gain for the bead classifier photodiode detectors (CL1 and CL2) and for the doublet discriminator detector (DD). The second calibrator (CAL-2) adjusts the gain for the reporter PMT (RP1). A current practice is to calibrate with CAL-1 to target values and calibrate CAL-2 to a fixed value, for example a value of approximately 17,000 irrespective of the target value. In one embodiment, the CAL-2 target value is around 3,800±10%. 
     In flow cytometry, electronic gating typically is used to isolate classes of cells or particles. Often, gating is used to differentiate one population of cells or particles from other populations. Doublet discriminator (DD) gating is also used to eliminate debris and aggregates from the counting statistics. The within-RV CV % values are lower when DD gates are used. In the case of the detector, differentiation is accomplished via region gating (CL1 and CL2) and there is a partial gate on the reporter channels that allows elimination of very low RFI events (usually between 0-2). DD gating is almost exclusively used by flow cytometers to eliminate debris and aggregates. 
     In addition to recording three different fluorescence measurements, MAD system  10  also detects light scatter. The collected scattered light is orthogonal scatter, also referred to as right-angle, side-angle, or wide-angle scatter. Orthogonally scattered light is a good reflection of the size of the particle from which the light impinged and was scattered. Side-angle scatter is easily capable of distinguishing a bead from a bead doublet (two beads stuck to each other or in very close vicinity). Detection of bead doublets is called doublet discrimination. In flow cytometry it is the usual practice to eliminate recorded doublet events from the data analysis since their physicochemical behavior is often aberrant when compared to single beads. Elimination of doublets can improve the precision and accuracy of an assay. When light impinges on a particle it is scattered without loss of energy in many directions. The magnitude and angles of scatter depend on such parameters as particle size, density, and shape. 
     Right-angle light scatter is detected on the MAD instrument with an avalanche photodiode, the same type of detector used to classify the beads into regions. 
       FIG. 8  schematically represents a process of washing microspheres  140 , or beads, using magnets  142 . Microspheres can be magnetic or have metallic properties or other properties that allow them to be attracted to magnets  142  during washing. When washing is required, reaction vessels  144  containing beads  140  in a solution  146  (e.g. a buffer solution or an assay reagent) are placed near two strong electromagnets  142  (e.g., in separation carousel  55  of  FIG. 3 ). Magnets  142  attract and hold beads  140  to the sides of the reaction vessel  144 . Liquid  146  is then aspirated from the reaction vessel leaving the beads on the vessel  144  sides attracted to magnets  142 . After removal of the magnets  142  as shown in  FIG. 8C , and beads are resuspended in another volume of liquid  146  as shown in  FIG. 8D . 
     5.3 Sample Processing Module (“SPM”) 
     5.3.1 General Features of SPM 
     Referring again to  FIG. 3 , one embodiment of sample processing module  30  can include a number of subsystems and components for automating sample handling and assay procedures of system  10 . Such subsystems can include a specimen rack handler assembly  50 , a reaction vessel handler assembly  52 , a reaction vessel supply system  54 , an incubator and separation carousel  56 , a reagent storage assembly  58 , a reagent robot  60 , a wash robot  62 , a solid waste system  64 , a sample handler  66 , and a fluidics system  68 . 
     Each of the various subsystems and their interactions are described in more detail in sections below. Each of these subsystems and their physical relationship to other subsystems and components within SPM  30  are described in the context of an exemplary embodiment of system  10 , and such examples are not intended to limit the invention. One skilled in the art will appreciate that variations in each subsystem and/or their interactions may be made without departing from the scope of the invention. 
     For example, in the embodiment of system  10  detailed below, SPM  30  includes twenty seven discrete stepper motors for actuation of various instrument robotic systems. These include multiple high speed high power carousel drives capable of better than, e.g., 0.5 sec positioning times, for moving incubation and separation carousel  56  and reagent carousel  70 . In addition, multiple X, Y robots having, e.g., at least 0.5 mm placement accuracy, preferably about 0.2 mm or better placement accuracy, are employed for driving specimen rack handler  50 , reaction vessel handlers  52 , reagent robot  60 , sample handler  66 , wash robot  62 , and detector transfer robot  74 . Additionally, Z-theta robots may be used to minimize probe movement times even further for time critical actions. One skilled in the art will appreciate that different number and types of subsystems and drive motors may be employed without departing from the overall spirit of the present invention. 
     Motor drives and sensor feedback are provided by a number (e.g., four or more) of custom designed stepper and sensor control printed wire assemblies (PWA&#39;s; also termed herein printed circuit boards, or PCB&#39;s), each capable of simultaneously driving multiple motors. Each has the capacity for multiple, e.g., up to 24, sensor inputs used for positional feedback and motor step loss detection. 
     As will be described in more detail below with respect to some subsystems, e.g., specimen rack handler  50 , RV handlers  52 , reagent robot  60  and incubator carousel assembly  56 , integrated circuit boards related to each subsystem of SPM  30  preferably communicate over an integrated compact PCI bus main system processor board of host computer  40 . The main system processor board of host  40  can be, e.g., a Pentium III or the like single board computer running at 850 MHz, with 128 Mbytes on board RAM and 48 Mbytes flash disk permanent storage. Alternatively host  40  can also be a remote server which the device communicates with over a network. The logging of operational data to a controlling host via USB minimizes the requirement for data storage on system  10 . 
     SPM  30  as described in the example below also incorporates four or more pipetting probes for manipulating samples and reagents, e.g., a sample handing probe associated with sample hander assembly  66 , a reagent probe associated with reagent robot assembly  60 , a wash dispense probe associated with wash robot  62 , and a detector probe associated with detector robot  74 . Sample handler  66  probe is used to aspirate and dispense samples from within tubes  167  on specimen rack handling assembly  50  into reaction vessels on incubation and carousel assembly  56 . Reagent robot  60  probe is used to aspirate and dispense reagents from reagent packages  80  in reagent carousel  70  into reaction vessels on incubation and separation carousel. In one embodiment, reagent robot  60  and sample handler  66  probes share a common tapered-tip design and are interchangeable. Wash robot  62  probe and is used to dispense wash solution into reaction vessels on incubation and separation carousel  56 . Detector robot  74  probe is used to aspirate the completed assay bead solution into detector  20  for analysis. 
     Each of the probes described herein are preferably made of stainless steel with an internal polished surface to reduce nonspecific binding. In one embodiment, internal diameter of sample handler  66  and reagent  60  probes at the tapered tip is 475±25 μm (e.g., approximately 60-fold wider than the diameter of the magnetic beads). All probes except the detector probe are preferably tapered and beveled. Sample handler  66  and reagent robot  60  probes preferably incorporate sensors such as capacitive liquid level sensors for accurate and repeatable sensing of the liquid surface height, as well as pressure sensing for detection of blockage and/or when a probe is in contact with the bottom of an empty vessel. 
     Additional details of each of the subsystems and major components of sample processing module  30  follow. 
     5.3.2 Specimen Rack Handler Assembly 
       FIGS. 9 and 10  depict a specimen rack handler assembly  50  (also referred to herein as “specimen handler” or “rack handler”) according to an embodiment of the present invention. Specimen handler  50  moves samples from an input area  150  through an instrument work area  160  to an output area  164 . In doing so, the specimen handler moves the samples into an aspiration position. The specimen handler identifies each rack  166  and sample tube  167  by reading a barcode contained on each. There is a STAT (Short Turn Around Time) drawer  156  that provides the user with a mechanism for inserting a rack  166  to be sampled and tested out of sequence. The specimen rack handler assembly  50  also allows for continued uninterrupted operation while a user adds or removes samples. 
     Specimen handler assembly  50  generally includes an input area  150 ,  151 , a main work area or horizontal platform  160 , a robotic finger  152 , a look-ahead offline platform  154 , a STAT drawer  156 , an aspiration offline platform  158 , a look-ahead barcode reader  162 , an aspiration offline barcode reader  164 , and sample trays and racks  166 . 
     Robotic Finger  152  is designed to move sample racks  166  along horizontal platform  160  without interfering with any of the other specimen handler  50  components. In one embodiment, finger  152  employs a 2-axis mechanism (horizontal in the x-axis and rotational). The two-axes work in conjunction to allow the finger to either push a rack (e.g., to the right or left) or bypass a rack. The horizontal axis provides the horizontal motion while rotational axis provides the option for either engaging or disengaging from pushing the racks. 
     Referring to  FIG. 10 , horizontal movement of finger  152  is belt-driven by a stepper motor  222 . This motor/belt drive assembly  222  is preferably located underneath the horizontal platform  160  to minimize its interference with other specimen handler  50  components and accessibility to users. 
     The rotational axis movement is also belt-driven by a stepper motor  226 . Motor  226  preferably rotates a square shaft (on which the horizontal motion occurs) of finger  152  to move finger  152  down to a disengaged position (as shown) or up into an engaged position. In the engaged position, finger  152  can slide racks  166  from right to left along horizontal platform as shown in  FIG. 9  under the power of horizontal stepper motor  222 . 
     The number of sensors monitor the position and status of the robotic finger  52 . A finger horizontal home optical sensor  223  located on farthest right side of the specimen handler  50  determines the horizontal home position of finger  52 . A Finger horizontal step optical sensor  224  located on the farthest right side of the specimen handler  50  determines the horizontal position of finger  152 . A finger rotational home optical sensor  228  located on farthest right side of specimen handler  50  determines the rotational home position of the finger  152 . A finger rotational step optical sensor  230  located on the farthest right side of the specimen handler  50  determines the rotational position of the finger  152 . Each of the motors  222 ,  226  and sensors  223 ,  224 ,  228 ,  230  is electrically connected to system  10  via backplane printed wire assembly  200 . 
     The look-ahead offline platform  154  is designed to move the racks (and associated specimen tubes) off the horizontal platform  160  and identify them for the host control  40  software. Look-ahead barcode reader  162  is used to read and identify barcodes of both samples  167  and rack  166  when the look-ahead offline platform pulls a rack  166  off horizontal platform  160 . 
     Scheduling software in host computer  40  optimizes the throughput of the instrument and uses the information provided by barcodes on each of the racks  166  and sample tubes  167 . 
     Movement of the offline look-ahead platform  154  is driven by an offline look-ahead motor  202 . Motor  202  moves platform  154  (and a rack  166  located thereon) in a y-axis direction (e.g., in a direction perpendicular to the long axis of horizontal platform  160 ) to present racks  166  and sample tubes  167  to bar code reader  162 . A number of optical sensors are present on the look-ahead offline platform  154 . For example, a look-ahead offline rack optical sensor  210  determines the presence of a rack  166  on the platform. This sensor  210  is located on the top rear of the look-ahead offline platform  154204 . A look-ahead offline platform home optical sensor determines the horizontal (y-axis) home position for the look-ahead offline platform. Sensor  204  is located behind the horizontal platform  160  near barcode reader  162 . A look-ahead offline platform step optical sensor  206  determines the horizontal (y-axis) position for the look-ahead offline platform. This sensor  206  is located behind the horizontal platform  160  on the rotational drive gear. Rack sensor  210  communicates with circuit board  208  and each sensor  202 ,  204 ,  206 ,  210  electrically communicates with system  10  through backplane  200 . 
     The STAT drawer  156  is designed to provide the user the ability to place a rack  166  (with samples  167 ) at the head of the queue for immediate processing by instrument  10 . Rack  166  is placed just prior to aspiration offline platform  158  so it will be moved onto platform  158  as soon as the current rack is finished. No other action is required by the user, aspiration offline platform  158  will automatically transfer the rack and sample information to the scheduling software in host  40 . 
     A sensor  234 , e.g., such as a mechanical plunger type sensor, located on the underside of STAT drawer  156  determines the status of the STAT drawer  156 . 
     The aspiration offline platform  158  is designed to move the racks (and associated specimen tubes) off the specimen handler  50  horizontal platform  160 , identify them for the software and provide an aspiration location for the sample handler assembly  66  (which includes a robotically-controlled sample aspiration probe). As with barcode reader  162 , aspiration barcode reader  164  associated with aspiration offline platform is used to identify both the rack  166  and individual tube  167  when aspiration offline platform  158  pulls them off of the horizontal platform  160 . Typically, this is just confirming the information obtained by barcode reader  162  of the look-ahead offline platform  154 , but occasionally, e.g., when STAT drawer  156  is used, barcode reader  162  will be providing new information to the scheduling software. 
     Similar to look-ahead platform  147 , aspiration or sample offline platform  158  is driven by a motor  212 . Motor  212  moves platform  158  (and a rack  166  located thereon) in a y-axis direction (e.g., in a direction perpendicular to the long axis of horizontal platform  160 ) to present racks  166  and sample tubes  167  to aspiration bar code reader  164 . 
     The number of optical sensors are present on the aspiration offline platform  158 . For example, an aspiration offline rack optical sensor  220  located on the top rear of aspiration offline platform  158  determines the presence of rack  166  on the platform. Aspiration offline home optical sensor  214 , e.g., located behind horizontal platform  160  near the barcode reader  164 , determines the horizontal (y-axis) home position for aspiration offline platform  158 . An aspiration offline step optical sensor  216 , e.g., located behind the horizontal platform on the rotational drive gear, determines the horizontal (y-axis) position for the aspiration offline platform  158 . 
     Sensor  220  communicates with rack sense circuit board  218 , and all of sensors  212 ,  214 ,  216 ,  164  and  218  communicate with backplane  200 . 
     Horizontal platform  160  is designed to provide a stable horizontal surface for rack movement, input and output areas  151 ,  162  for sample trays, and manual rack input  150  and output  164  areas  150 ,  164 . 
     Manual input area  150  provides the ability to add single racks  166  to the queue. Manual input area  150  is located at the far left of specimen handler assembly  50 . When a rack  166  is placed here, sensor  220  is tripped notifying software in host  40 . Finger  152  moves the rack  166  to the end of the queue. An optional manual input optical sensor  146 , e.g., located behind the back wall of the specimen handler  50 , includes a mirror mounted on the specimen handler  50  front. Placement of a rack  166  in manual input area  150  breaks the reflected beam of sensor  246 . 
     Input tray area  151  provides a location for the placement of a sample tray  165 . Once a sample tray  165  is placed, it essentially becomes part of horizontal platform  160  over which racks  166  are moved. 
     Input tray area sensor  252 , e.g., located underneath specimen rack handler assembly  50 , is preferably a magnetic reed type sensor. Sample trays  165  are equipped with magnets in the base to trip sensor  252  when the sample tray  165  is properly placed. 
     Look-ahead area  155  provides a storage area for racks  165  awaiting aspiration. Output holding area  157  provides an output area for racks (after sample aspiration). Typically, output holding area  157  will only have racks when the output tray  162  is missing or full. 
     Output tray area  162  provides a location for the placement of a sample tray  165 . Output tray area sensor  232 , e.g., located underneath specimen rack handler  50 , is preferably a magnetic reed type sensor similar to sensor  252 . As described above, sample trays  165  are equipped with magnets in the base that trip sensor  252  when such sample tray  165  is properly placed. An optional output tray capacity sensor, e.g., located behind the specimen handler  50 , monitors how many racks  165  are on the output tray  162 . After a specified number of racks, e.g., ten, have moved onto output tray area  162 , such sensor trips software in host  40  to request the customer to remove and empty the output tray. 
     Manual output area  164  provides a location for the removal of single racks  166  from the output area  162 . 
     In one embodiment, sample trays  165  are designed to carry ten racks  166 . Sample trays  165  allow large numbers of racks  166  to be added to or removed from the instrument  10  with ease. When not in the instrument (being carried) a self-locking mechanism is used to ensure the racks  166  cannot inadvertently slide off from the tray  165 . The self-locking mechanism automatically unlocks when the rack is placed on the instrument  10  or on a flat surface. 
     During typical operation of specimen handler assembly  50 , sample tubes  167  are loaded into racks  166  that contain up to five bar-coded sample tubes in each rack. Optionally, racks  166  are loaded into a tray  165  that hold up to ten racks in a queue awaiting tube barcode reading and sample processing. Controls and calibrators are also loaded into the same racks and are appropriately barcoded for identification. After tray  165  is placed in the input tray area  151  on horizontal platform  16 , input tray sensor  252  detects tray  165 . Finger  152  retracts and moves all the way to the left of manual input area  150 . Finger  152  then rotates to the horizontal position, and moves racks  166  to the right until the look-ahead rack sensor  210  detects a rack on the look-ahead offline platform  154 . Look-ahead offline platform  154  retracts, allowing the look-ahead barcode reader  162  to read the barcodes. 
     After reading the barcodes, the look-ahead offline platform  154  returns to the original position. Finger  152  moves the rack off the look-ahead offline platform  154  and onto the look-ahead area  155 . The rack is here until aspiration offline platform  158  is available. Once the aspiration offline platform is available, finger  152  moves the rack onto aspiration offline platform  158  until the aspiration rack sensor  220  detects the rack on aspiration offline platform  158 . Aspiration offline platform  158  then retracts into SPM  30  allowing the aspiration barcode reader  164  to read the barcodes. 
     Next, specimen robot  66  (see  FIG. 3 ) obtains samples from the sample tubes  167  in the rack  166 . Aspiration offline platform  158  then returns to the original position. Finger  152  moves the rack off the aspiration offline platform  158  to the output area  164 . The rack is held in the output holding area  164  until the output tray area  162  is available. Finger  152  moves the rack onto a tray in output tray area  162 . Finally, the output tray is removed from instrument  10 . 
     5.3.3 Reaction Vessel Handling and Supply Assembly 
     Referring to  FIG. 11 , reaction vessel handing and supply assembly  260  generally includes a reaction vessel supply  262  (“RV supply  262 ”) and two reaction vessel handlers  52   a  and  52   b . RV handlers  52   a ,  52   b  and their associated motors and components are also collectively referred to herein as RV handler sub-assembly  52  or simply RV handlers  52 . 
     5.3.3.1 Reaction Vessel Supply 
       FIGS. 11-16  depict a reaction vessel supply system  262  according to an embodiment of the present invention. Reaction vessel supply system  262  generally includes a reaction vessel supply bin  264 , or hopper, a reaction vessel supply motor  266 , belt  268 , fans  270 , and belt guards  272 . Reaction vessel supply system  268  stores enough reaction vessels to supply device  10  for a long period, e.g., six or eight hours or more, of continuous operation. Reaction vessel supply system  262  also presents reaction vessels to a position where the reaction vessel handlers  52   a ,  52   b  can retrieve them. The maximum time interval between presentations of reaction vessels to pick up position is preferably 45 seconds or less, more preferably 33 seconds or less. Reaction vessel supply system  262  stores reactions vessels in a clean environment such that the reaction vessels do not become contaminated and interrupt the integrity of results of device  10 . 
     Referring to  FIGS. 12-14 , RV storage sub-system  262  includes a lugged belt that loops through bulk storage bin  264 , or hopper  264 , which has a funnel shaped section  274  at its bottom. A geared down stepper motor  266  is used to drive belt  268  through storage bin  264 , mixing RVs and collecting RVs with pick up lugs  269  attached to belt  268 . RVs that are picked up and reach the top of the belt&#39;s  268  travel are detected by an optical through beam detector  280 . Two static wedge shaped belt guards  272  and a fan style blower  270  with duct  271  remove RVs that are incorrectly presented by lugs  269  before they reach optical beam detector  280 . Lugged belt  268  is stopped whenever a RV is detected. RV handler  52   a  is then used to transfer the detected RV into incubator carousel  57  for use in the assay process. 
     The RV supply bin  264  includes a front-loading style door  265  that acts as a chute, when opened, to gather any errant RVs. The operator can add RVs to the RV Supply (without interrupting instrument operation) at any time by simply opening door  265  and adding RVs. RV supply belt  268 , also known as hopper belt  268 , is located at the rear of the RV supply bin  264 . 
     RV supply bin  264  has two sensors  276 ,  278  to determine the RV level in supply hopper  264 . Sensors  276 ,  278  are preferably infrared through beam sensors. In one embodiment, sensors provide feedback when the RV level drops below an amount sufficient to provide a specified amount of run time, e.g., over an hour of instrument run time at 100 RVs per hour, and to detect when the RV supply bin  264  has been refilled. For example, the “high” sensor  278  might detect an approximate RV full level as approximately 800 RVs and “low” sensor  276  might be set for approximately 200 RVs. 
     Referring to  FIGS. 13A-13C , the presence of an RV  290  in a belt lug  269  is determined by RV presentation optical sensors  280   a  and  280   b . These sensors determine when RV  290  has been picked up by RV Supply belt  268  and has arrived at the presentation position  282  (location where RV Handler  52   a  picks up supply RVs). These sensors  280   a ,  280   b  are located at the top of the supply belt  268 . 
     In one embodiment, sensors  280   a  and  280   b  are dual infrared through beam sensors that permit differentiation between a lug  269  containing a RV  290  (as shown in  FIG. 13A ) and an empty lug. Beam sensors  280   a ,  280   b  are positioned so that RV  290 , if present, breaks the beam of sensor  280   a  and beam of sensor  280   b  is broken by belt lug  269 . 
     As an empty lug  269  passes through the detection point  282  sensors  280   a  and  280   b  see the logic pattern in  FIG. 13B . As a lug  269  containing a RV  290  passes through the detection point sensors  280   a  and  280   b  see the logic pattern in  FIG. 31C . The dotted line indicates when the hopper control software would stop the belt  268  and wait for the RV handler  52   a  to remove RV  290 . Both through beam sensors  280   a ,  280   b , preferably employ a modulated signal to reduce sensitivity to ambient light conditions. 
     Referring now to  FIG. 14 , RVs are moved from the supply bin  264  to the presentation point  282  by a motor  266  and belt  268  drive system. Motor  266  is preferably, although not necessarily, located below supply bin  264  as shown. Motor  266  and its associated gears, e.g., lower pulley  288  and drive belt  271 , move lug belt  268  around lower and upper pulleys  288  and  291 , respectively. As belt  268  turns, lugs  269  move through RV supply bin  264  and pick up RVs  290 . Lugs  269  are preferably specially designed to pickup one RV  290  at a time regardless of the RV&#39;s orientation within the supply bin  264 . 
     Fan  270  and belt guards  272  are designed to ensure that only one RV is presented to RV Handler  52   a . Fan  270 , here mounted on the side of the RV Supply Bin  264 , essentially blows any incorrectly positioned or additional RVs off belt lugs  269 . Belt guards  272 , located in the vertical corridor between the RV supply bin and presentation point  282 , provide a direct physical barrier to incorrectly positioned or additional RVs on belt lugs  269 . Additionally, a stainless steel rooftop may be mounted to the Supply Bin body to physically remove any improperly positioned RVs. 
     Referring to the block diagram of  FIG. 15 , optical sensors  280   a ,  280   b  and hopper sensors  276  and  278  are associated with one or more printed wire assemblies, e.g., PWA  284 , which communicates with backplane  200 . In addition, RV supply motor  266  and belt  268  are monitored by RV supply step optical sensor  286  to determine if step-loss is occurring during movement of belt  268 . In this embodiment, sensor  286  is preferably located on rotational gear  288  used to move the belt. When a step-loss (error or collision) is detected, the drive current to motor  266  is removed in an effort to minimize the possibility of damaging carousel  56  or the object it has collided with. During the movement of motor  266 , the control software calculates the exact time when the encoder will be in the middle of either a slot or the adjoining rib. The software then checks at each calculated time to compare the sensor  286  state to the predicted state. If a discrepancy is detected, a position error is reported. 
     In one embodiment, reaction vessels are presented within the following approximate tolerances: Z-axis, +/−1.0 mm; Y-axis, +/−1.0 mm, X-axis, +/−0.5 mm. In some cases, such tolerances may be preferable to help avoid reaction vessel jamming in the pickup lugs or not being correctly placed into incubation carousel  57 . 
     The drive torque applied to the belt may be increased by the use of a reduction drive, e.g., a 15:80 or similar reduction drive, on motor  266 . Also, belt pulleys  288 ,  290  preferably have ridged edges to maintain belt alignment and are preferably mounted with their axes approximately square to belt  268  centerline. A user interface, e.g., interface  44  on computer  40 , notifies a user when the RV supply hopper  264  needs to be refilled. 
     Optionally, the RV supply assembly  260  includes a timeout feature. For example, if the RV belt  268  is unable to pickup and present a RV within a defined period of time, e.g., 30 or more seconds from the last presentation, the RV supply assembly  260  will cease operation and the instrument  10  will notify the user via the user interface  44 . 
     In use, host computer  40  or a control subsystem determines that an RV is required and causes stepper motor  266  to drive belt  268  through supply bin  264 , mixing RVs and collecting RVs with pick-up lugs  269 . RVs that are improperly picked up or positioned, are then removed by belt guards  272  and a fan  270  before they reach presentation point  282 . At presentation point  282 , optical beam detectors  280   a ,  280   b  detect the presence of an RV  290  and a lug  269 . The lugged belt is stopped when a RV  290  is detected within a lug  269 . RV handler  52   a  then transfers the presented RV  290  into incubator carousel  57  for use in the assay process. 
     5.3.3.2 Reaction Vessel Handlers 
       FIGS. 16 to 21  show a reaction vessel handler sub-assembly  52  according to an embodiment of the present invention. Reaction vessel handler assembly  52  generally includes horizontal drives  302   a ,  302   b  and vertical drives  304   a ,  304   b , gripper assembly  306   a ,  306   b , and horizontal tracks  300  on common gantry  72 . Reaction vessel handler assembly  52  moves reaction vessels  290  from various locations to other locations, automatically aligns the reaction vessels  290  at pick-up, detects the presence of reaction vessels held within the gripper assembly  306   a ,  306   b , and provides feedback of RV handler  52   a ,  52   b  location and status to the computer  40 . In a preferred embodiment, reaction vessel handler assembly  52  includes two reaction vessel handlers  52   a ,  52   b , operating simultaneously to increase the efficiency and speed of system  10 . 
     Referring back to  FIG. 3 , RV handler assembly  52  cooperates with specimen rack handler  50 , incubation and separation carousel assembly  56 , RV storage supply  262  and RV waste  64  assemblies. Each RV handler  52   a ,  52   b  interfaces with different components of the instrument  10 . In some cases, they may interact with the same component but they do so at different locations. TABLE 1 provides examples of RV handler  52   a ,  52   b  interaction with other components. Additional details of the interaction between the various component modules and subassemblies will be described herein in more detail in later sections. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Reaction Vessel Handler Interactions 
               
            
           
           
               
               
               
            
               
                   
                 RV Handler 
                 Interacts with 
               
               
                   
                   
               
               
                   
                 RV Handler 52a 
                 RV Supply 262 
               
               
                   
                   
                 RV Waste 64 
               
               
                   
                   
                 Detector Transfer Robot 74 
               
               
                   
                   
                 Separation Carousel 55 
               
               
                   
                   
                 Incubator Carousel 57 (all three rings) 
               
               
                   
                 RV Handler 52b 
                 Separation Carousel 55 
               
               
                   
                   
                 Incubator Carousel 57 (two outer rings only) 
               
               
                   
                   
               
            
           
         
       
     
     Referring to  FIG. 17 , each of the RV handler mechanisms  52   a  and  52   b  includes a common horizontal linear travel axis  300  (y-axis) upon a common gantry  72  and separate but preferably, although not necessarily, similar gripper assemblies  306   a  and  306   b , which include a vertical linear axis (z-axis) and gripping axis (theta axis). 
     Each RV Handler  52   a ,  52   b  is associated with a horizontal drive  302 , a vertical drive  304 , and a gripper assembly  306 , respectively. Note that because RV handler  52   a ,  52   b  include essentially the same components and sub-assemblies, the terms RV handler assembly  52 , horizontal drive  302 , vertical drive  304 , gripper assembly  306 , etc., are occasionally used herein without using “a” or “b” to designate a particular RV handler. 
     Horizontal Drives  302  move the RV Handlers  52  horizontally (e.g., along y-axis) along gantry  72 . Motor  266  and associated gearing are mounted on the stationary gantry  72 . RV Handlers  52  are attached by slide  309  to rail  300  and attached to motor  302  by belt  312  such that motor  302  and associated gearing drive belt  312  and move RV handler along rail  300 . 
     The horizontal range of motion for RV Handler  52   a  is constrained to travel over the RV supply  262 , incubator carousel  57  (e.g., forward half only), separation carousel  55  and the detector robot  74 . The horizontal range of motion for RV Handler  52   b  is constrained to travel over incubator carousel  57  (rear half only) and separation carousel  55 . 
     Horizontal drive  302  preferably has two sensors to determine its position. A horizontal home optical sensor preferably determines the horizontal home position of the RV handlers  52 . Horizontal step optical sensor preferably determines the horizontal position of the RV Handlers  52 . Both sensors are preferably located on gantry  72 . 
     Vertical Drive  304  moves grippers  307  vertically (z-axis) on the RV Handlers  52   a ,  52   b . Motor and gearing of vertical drive  304  are mounted in the moving RV Handler  52   a ,  52   b . Gripper assembly  306  rides on a rail bearing  316  (located vertically within the RV Handler  52 ) and is attached to the motor and gearing  304  by a belt  318  and pulleys  317 ,  319 . In this embodiment, although not necessarily, vertical range of motion for both RV handlers  52   a ,  52   b  is approximately the same and constrained by hard stops  315  located at the end of the rail bearing. 
     To prevent RV handlers  52  from dropping a RV when the power is interrupted (either power loss or e-stopped), the vertical drive control circuitry incorporates a dynamic braking feature preferably. During dynamic braking, gripper head  306  is prevented from free falling by the back EMF created in the motor winding. The dynamic braking circuitry works by shorting the windings of the vertical axis stepper motors with a relay connected to the 24V power supply. Since the drive current to the stepper motor is provided by the same power supply it ensures that dynamic braking is enabled as soon as the drive current is interrupted. 
     Vertical drive  304  has two sensors to determine its position. A vertical home optical sensor, preferably located on the RV handler  52  determines the vertical home position of the RV Handler. A vertical step optical sensor, also preferably located on RV handler  52 , determines the vertical position of the RV handler  52 . 
       FIG. 18A-C  shows additional detail of gripper head assembly  306  with  FIGS. 18A and 18C  having gripper drive motor  305  and support bracket  332  removed. In this embodiment, gripper assemblies  306  employ a cam driven scissor  330  mechanism actuated by a stepper motor  305 . The motor  305  and cam are mounted on the gripper assembly  306 . Gripper assembly  306  uses coil springs  320  and specially designed gripper jaws  307  to provide a consistent gripping force and compensation for misalignment of RVs. 
     Sealed ball bearings can be are used in both jaws to prevent wear and increase alignment accuracy. Due to the light axial spring load on the gripper jaws  307  no spacer has been used in this embodiment to separate the bearings in each jaw. Both jaws are lightly spring  320  loaded against the alignment/pivot pin  336 .  FIG. 18B  shows the alignment pin  336 , gripper jaws  307  and spring  320 . A nyloc nutsert  338  prevents pivot pin  336  from moving. The thread on the alignment pin is preferably cut undersize to permit alignment to the gripper motor bracket  332 . 
     Referring to  FIG. 18C , gripper assemblies  306  use one or more, e.g. two, optical sensors  332 ,  334  to determine if an RV  310  is present in the gripper jaws  307 . Sensors  332 ,  334  are located on each RV Handler  52   a ,  52   b . Each sensor  332 ,  334  monitors one side of gripper jaws  307 . 
     In one embodiment, flexible wire cables are used to prevent fatigue failures for the moving components on the vertical and horizontal axes. The thin nature of the cable helps minimize stresses within the wires thus maximizing fatigue life. The cables are capable of, e.g., greater than 5,000,000 moving cycles with a minimum bend diameter of approximately 40 mm or more. The cables are preferably constrained in both the vertical and horizontal directions to limit bending. The cables are also routed to avoid rubbing on potentially damaging surfaces. Strain relief is provided by mechanically clamping the cables to a connection point. 
     Gripper jaws  307  are aligned in the x-axis (e.g., left to right in  FIG. 18B ) by adjusting alignment pin  336  that runs through the gripper jaws. 
     Referring to  FIGS. 19A and 19B , in one embodiment gripper jaws  307  include two jaw pieces  307   a  and  307   b . Each jaw piece  307   a  and  307   b  includes grip features, e.g.,  340 ,  342 ,  344 ,  346 ,  348  and  350 , to position and hold RVs. Examples of grip features for a primary  307   a  and secondary  307   b  jaw piece are shown, however other grip patterns or features may be used. In this embodiment, primary jaw  307   a  of  FIG. 19A  includes two contoured grip features  340  and  342  configured to position and hold RVs in a vertical orientation. A rib  344  helps prevent upward sliding of an RV. Secondary jaw piece  307   b  includes a single point of contact  348  that contacts the side of an RV and helps hold it against features  340  and  342  of primary jaw. A second, smaller, feature  346  only contacts the upper flange of an RV (see  FIG. 21 ) if the RV is pulled vertically out of jaws  307 . An upper rib  350  prevents upward shifting of an RV in the event of a collision. 
     Referring to the block diagram of  FIG. 20 , motors  302 ,  304  and  305  of RV handlers  52   a  and  52   b  communicate with backplane circuit board  200  through RV handler gantry circuit board  356 . RV handler vertical motor  304  communicates through RV handler head circuit board  354 . Gripper motor  305  communicates with gripper motor board  352 , which communicates with RV handler head circuit board  354 . One skilled in the art will appreciate that a different arrangement of circuit boards or other control features may be employed. 
     5.3.3.3 Reaction Vessel (RV) Design 
     Referring to  FIG. 21 , a typical reaction vessel  290  according to the present invention employs a non-nesting design compatible with the hopper style RV supply system  262  described herein. RV  290  generally is dimensioned as a tube or vessel having a body  368  and an open end  360 . External ribs  366  at end of RV opposite opening  360  help prevent nesting with other RVs. In addition, a flange  362  provides an upper stop surface for grippers  307  and extends internally to form a lip on the inside of RV opening to further reduce possibility of RV nesting. A locating shoulder  364  provides a lower stop surface for grippers  307  and may be used to support RV  290  when placed in a nest or carousel such as incubation and separation carousel  56 . RV  290  preferably includes similar internal geometry as the existing B-R RVs (BIO-RAD part no. 223-9391) over the bottom half of the RV. 
     5.3.3.4 Operation of Reaction Vessel Handling and Supply Assembly 
     During use, RV Handler  52   a  removes an RV  290  from RV Supply  260  as described previously and places RV  290  in incubator carousel  57  (see  FIG. 3 ). Then, sample and reagent are added to RV  290  using sample handler assembly  66  and reagent robot assembly  60 , respectively as described below. RV  290  is incubated for a specified amount of time (chemistry dependent). RV Handler  52   b  then moves RV  290  from the incubator carousel  57  to the separation carousel  55 , where the sample undergoes a wash and separation process within RV  290 . 
     After the wash and separation process, RV Handler  52   b  moves RV  290  from separation carousel  55  back to incubator carousel  57 . Additional reagents or conjugates are added if need. Incubation and washing are repeated as required by the particular assay. After assay preparation is complete, RV handler  52   a  then moves the RV  290  from the incubator carousel  57 , or in some cases from wash and separation carousel  55  or some other location, to the detector transfer robot  74 . Typically, interaction of RV  290  with the RV handlers  52   a ,  52   b  is finished at this point. 
     Each RV Handler  52   a  and  52   b  is capable of adjustment and alignment with other components of system  10 . For example:
         Alignment of RV handler  52   a  to the incubator carousel  57  (all three rings) in the x-y-z directions.   Alignment of RV handler  52   a  to the separation carousel  55  in the x-y-z directions.   Alignment of RV handler  52   a  to the detector robot  74  in the y-z directions.   Alignment of RV handler  52   a  to RV supply  260  in the y-z directions.   Alignment of RV handler  52   a  to RV waste  700  in the y-z directions.   Alignment of RV handler  52   b  to the separation carousel  55  in the x-y-z directions.   Alignment of RV handler  52   b  to the incubator carousel  57  (two outer rings only) in the x-y-z directions.
 
5.3.4 Specimen Handler Assembly
       

       FIGS. 22-24  show a specimen handler assembly  66 , also termed herein “sample handler assembly  66 ”, “sample handler  66 ” or “specimen handler  66 ”, according to an embodiment of the present invention. Sample Handler assembly  66  includes a number of subsystems and components, including a specimen probe  370  (also termed “sample probe”), a sample robot  380 , a sample liquid level sensor  390 , a blockage detection sensor  392 , and a clean station  90 . 
     Specimen probe  370  is designed to aspirate and dispense specimens and be easily cleaned in clean station  90 . Sample robot  380  preferably includes a probe mount  376  for holding sample probe  370  and moves probe  370  in the y and z directions, e.g., horizontally along gantry  72  and rail bearing  382  and vertically to engage sample tubes  167  and RVs  290 . Similar to RV Handlers  52 , which are located on opposite side of gantry  72 , sample robot  380  is driven by a horizontal and vertical motors such as stepper motors  384 ,  386  (see  FIG. 23 ). One or more optical sensors  388  provide accurate monitoring of probe  370  position. 
     Generally, sample handler  66  aspirates a sample from the specimen rack handler  50  and dispenses the sample into an reaction vessel  290  held on incubator carousel assembly  56 . Sample handler  66  monitors specimen probe  370  for any loss of function or blockage, minimizes dead volume required using liquid level sensing, and minimizes the amount of sample used. Sample handler assembly  66  also cleans the specimen probe  370  to minimize any carryover between samples and/or reagents and provides the ability to sample various volumes. 
     5.3.4.1 Sample Probe 
     Sample, or specimen, probe  370  is designed to aspirate and dispense samples and undergo easily cleaned. Referring to  FIG. 23 , sample probe  370  includes a head  372  for engaging with probe mount  376  of robot  380  ( FIG. 22 ) and a tapered tip  374 . Internal diameter of the lumen  376  of probe  370  is preferably reduced at tip  374  to enhance dispense accuracy. Sample probe preferably uses a dual cavro pump system (discussed below with respect to system fluidics) to aspirate, dispense and clean. A smaller, e.g., 250 μL, syringe performs the aspiration and dispense functions while a larger, e.g. 2.5 mL, syringe performs the cleaning function. Probe lumen  376  is fluidly connected with system  10  fluidics through tube  378  (see  FIG. 22 ) attached to probe mount  376 . In a preferred embodiment, sample probe  370  is replaceable and shares a common design with reagent probe  61 . Additional features of the sample/reagent probes are described in section 5.3.5 below. 
     Sample probe  370  is preferably mounted on an electrically insulated material, which facilitates the operation of the sample handlers liquid level sensing (LLS) system  390  described below. 
     5.3.4.2 Sample Robot 
     Sample robot  380  is designed to mount the sample probe  370  and move the probe in vertical and horizontal directions along gantry  72 . Referring to  FIG. 24 , stepper motors  384  and  386  provide the motion in each axis using a pre-tensioned belt (e.g., belt  383  of  FIG. 23  connects to horizontal motor  384  on opposite end of gantry  72 ). Optical sensors provide accurate monitoring of the probe position. For example, a horizontal step optical sensor  388  determines the horizontal position of sample robot  380 . This sensor is preferably located on the gantry. Optionally, a horizontal home optical sensor also located on gantry  72  determines the horizontal home position of the sample robot  380 . Similar to RV handlers  52 , vertical home optical sensors and vertical step optical sensors can be located on sample robot  380  may be used to determine the vertical home position and instantaneous position, respectively, of robot  380 . 
     5.3.4.3 Sample Liquid Level Sensing (LLS) and Blockage Detection 
     The LLS system  390  is designed to detect the entrance and exit of the sample probe  370  from liquid. The LLS uses the change in capacitance that occurs when a probe enters or exits liquid. Due to the small change in capacitance that occurs, stray capacitance is minimized by electrically isolating the sample probe  370  using a relatively non-conducting probe head  372  and mount  376  compared with conducting body of probe  370 . 
     Sample blockage detection  392  includes a pressure sensor that monitors the pressure variations that occur during aspirating or dispensing samples. The pressure ranges that occur during normal (good) aspiration and dispense are well known. When a probe becomes blocked the pressure variations change and fall outside of the known values. When this occurs, an auto-recovery is initiated by host  40 . Probe  370  is cleaned using pre-defined protocols. If this does not correct the problem, the user is notified to take corrective action. 
     5.3.4.4 Clean Station 
     Referring again to  FIG. 23 , clean station  90 , mounted on SPM  30  chassis near the incubation and separation carousel  56 , is designed to clean probe  370 . Probe  370  is cleaned before and after each sample aspiration and dispense. To achieve the carryover specifications, a two stage clean station  90  is used. In the first clean stage, probe  370  discharges directly into drain  400  (which carries contaminated liquid away). Then, in the second clean stage, the probe moves into a well  402  where liquid  404  (e.g., wash buffer) is pumped through the probe and fills well  404 . In this stage, the inside and outside of probe tip  374  are washed. Vacuum extraction through port  402  is used to remove used wash fluid  374 . 
     5.3.4.5 Example of Operation of Sample Handler Assembly 
     In use, after sample probe  370  is cleaned in the clean station  90 , probe moves vertically to the home position over a specimen rack located on aspiration platform  158  of rack handler  50 . Robot  380  moves probe  370  vertically down until specimen liquid is detected by the LLS system  390 . After liquid detection, the sample robot  380  moves a fixed distance further into the liquid and the specimen is aspirated. During aspiration, blockage detection system  392  monitors the aspiration pressure to determine if the sample probe is blocked (either partially or completely). Additionally, during aspiration the sample robot  380  moves the probe down to ensure the probe stays in the liquid. After aspiration, sample robot  380  moves to vertical home position. During this movement, the LLS system monitors the liquid level to ensure the probe exit from the liquid is at an expected position. 
     Specimen handler assembly  66  then moves horizontally along gantry  72  to incubator carousel  57  and down to set position for specimen dispense. The specimen is dispensed into an RV on the incubator carousel  57 . Sample Robot  380  then moves sample probe  370  back up to the vertical home position. Specimen handler assembly  66  moves horizontally back to clean station  90  stage one clean position  400 . Sample robot  380  then moves sample probe  370  down to the clean station  90  and discharges the over-aspirate volume and a set amount of buffer into clean station  90 . Sample robot  380  moves sample probe  370  to the stage two clean position  374 . Wash Buffer is pumped through the sample probe  370  into the clean station  90  to clean both the inside and outside of the probe. Finally sample robot  380  returns to the vertical home position. 
     5.3.5 Reagent Storage Assembly 
     5.3.5.1 Overview of Reagent Storage Assembly 
       FIGS. 25-32  depict the components and relative functions of a reagent storage assembly  58  according to an embodiment of the present invention. In particular,  FIGS. 25 and 26  depict reagent storage assembly with storage lid  412  open ( FIG. 25 ) and closed ( FIG. 26 ). Reagent storage  58  generally includes a reagent cooler  410 , rotational and agitation drives  440 ,  441 , a barcode reader  442 , reagent carousel  70 , pack piercer  420 , and a pack lid opener  430 . The reagent storage generally stores reagents under favorable conditions. Preferably, the temperature of the reagent storage is at least about 8° C. and at most about 10° C. Reagent storage  58  also maintains bead homogeneity, preferably within about ±5 percent, both horizontally and vertically, within the reagents. Reagent storage  58  also preferably can store up to 20 reagent packs within a removable carousel. The reagent storage preferably maintains performance characteristics in an ambient temperature of at least about 15° C. and at most about 30° C. Reagent storage minimizes dead volume within reagent bottles, minimizes reagent loss through evaporation, identifies reagent packs with barcodes, allows a user to change individual reagent packs and/or change or remove the entire reagent carousel  70 . Furthermore, reagent storage automatically opens reagent pack covers to aspirate reagents and automatically pierces the reagent bottle caps prior to reagent aspiration. 
     In one embodiment, the reagent carousel  70  preferably includes twenty or more variable reagent pack or kit positions  456 . Two or more of the positions preferably contain a detector clean kit (70% isopropyl alcohol) and a detector calibration kit (two bead sets stored in separate bottles). The assay panel reagent kits each preferably contain up to four liquid reagents. Also, the reagent motor movement is bi-directional. The reagent carousel is chilled to about 2-8° C. while the assay incubator is kept at about 37° C. (±0.5° C.). The temperature of the refrigerated reagent compartment is maintained by compressed liquid refrigeration mounted beneath the incubator. 
     Additional details regarding components and sub-assemblies of reagent storage assembly  58  are described below. 
     5.3.5.2 Reagent Cooler 
     Reagent cooler  410  maintains a relatively constant ambient temperature, e.g., between approximately 8° C. and 10° C., within the reagent storage  58 . Reagent cooler  410  accomplishes this using an insulated housing  411  and a vapor compressor  445  or other refrigeration mechanism to cool the reagents. 
     In one embodiment, cooler  410  includes a 12/24V vapor compressor  445  unit with a charge of, e.g., 132A refrigerant, an air-cooled condenser to dissipate heat, a fan to force air through the condenser, a drier to remove excess moisture from the refrigerant, a capillary tube expansion valve, a stainless steel tub evaporator  411  or housing which surrounds the reagents and provides cooling, insulation  413  around the evaporator tub to provide insulation and prevent external condensation; and an insulating lid  412  to prevent heat flow into the system. 
     Evaporator tub  411  is preferably stainless steel or the like and surrounded by structural foam insulation  413 . The stainless steel provides high durability and consistency of manufacture, while the structural foam minimizes the heat conducted into the refrigeration system through the evaporator walls and reduces condensation on the exterior surfaces of the reagent storage  58 . A structural foam thickness of approximately 17 millimeters is desirable to helps prevent potential condensation under ambient conditions of 40° C. and 90% RH, however other types and thicknesses of insulation may be used. A capillary tube can be used as a refrigeration expansion valve. 
     Reagent cooler lid  412  provides insulation for the top of reagent cooler  410 , and access to the reagent carousel  70  for the reagent probe  60 , reagent pack piercer  420 , and reagent pack lid opener  430 . In a preferred embodiment, reagent cooler lid  412  is moved by the same motor and drive assembly as the pack piercer  420  discussed below. A lid home optical sensor, e.g., similar to other optical sensor described herein, determines the home position of lid  412 . This sensor preferably is near pack piercer/lid motor and gearing  446 . 
     5.3.5.3 Rotational and Agitation Drives 
     Referring to  FIG. 26 , rotational drive  440  is a belt-driven turntable powered drive motor. In one embodiment, rotational drive employs a 48-volt motor, although other motors may be used. Rotational drive  440  moves rotates carousel the reagent packs (rotationally) to the various positions required for pack piercing, reagent aspiration and pack presentation (for replacement). 
     Agitation drive  441  performs the two functions of agitating the reagent bottles and lifting the reagent carousel  70  up to the installation/removal position. Preferably, the same drive motor is used in both functions. A simple clutch of two pins (moving in slots) on a lead screw/sun gear assembly  450  (e.g., see  FIG. 27B ) is used to accommodate each function. The agitation drive  441  agitates the reagent bottles by rotating lead screw/sun gear assembly  450 ,  451 , e.g., a the 75-millimeter lead screw/sun gear assembly  450 ,  451 , back and forth. The sun gear  451  then rotates two rows of planetary gears  452 , which include heads  453  upon which the reagent bead bottles sit. 
     Planetary gears  452  include a plastic bushing, which sits on a stainless steel bearing, to eliminate potential corrosion. Planetary gears  452  are supported on 3 mm stainless steel pins with spherical tops. In a preferred embodiment, sizing and finish of the pin was chosen to minimize wear between the pin and the hub of the planetary gear. The pin length was chosen to elevate the planetary gear hub above any fluid that may be present in the drive mechanism. 
     The motor agitation  441  lifts or lowers the reagent carousel  70  by rotating pins (in either direction) and engaging the lead screw. Once the pins have engaged the lead screw/sun gear  450 ,  451 , the reagent carousel  70  is raised or lowered. To balance the friction forces while raising and lowering the lifting platen  455 , vertical guide pins  457  are positioned symmetrically on the turntable. In this embodiment, a 75 mm lead screw  450  was chosen to provide stability for the lifting platen  455  in the raised position. The lead screw/sun gear  450 ,  451  and platen gear materials were selected for their noise and wear reduction properties. Example gears and suggested suitable materials are listed below in TABLE 2. 
     An agitation drive home optical sensor located on the rotational gear driven by the agitation drive motor  440  can be used to determine the rotational home position of the Agitation Drive. 
     An agitation drive proximity sensor can be used to determine a vertical home position of the agitation drive  441  and to determine if a reagent carousel  70  is loaded. This sensor is preferably located on a post that penetrates the tub floor. 
     The vertical position of the lifting platen  455  can be determined by rotating the turntable to align a pin, e.g., steel pin  457  on the bottom of the lifting platen and the proximity sensor. The lifting platen  455  can then be homed by lowering the platen until the pin  457  actuates the proximity sensor. The proximity sensor detects the presence of a reagent carousel  70  by detecting one or more pins, for example four steel pins, that are pushed to the same level as the home steel pin when a reagent carousel is loaded. In one embodiment, proximity sensor is a reed switch. 
     A rotational drive home optical sensor can be used to determine the rotational home position of rotational drive  440 . This sensor is preferably located on the rotation gear driven by the rotational drive motor. 
     The addition of a reagent pack to carousel  70  may cause the agitation drive to agitate the reagent packs continuously for four minutes to ensure the complete suspension of the bead. 
     5.3.5.4 Barcode Reader 
     Referring to  FIG. 27B , reagent pack barcode reader  442  views barcodes on reagent packs  80  (See  FIG. 28 ) through a heated window  443  on the reagent cooler  410 . In one embodiment, barcode reader  442  type is a MICROSCAN 710 reader. Other barcode readers are known and may be suitable. 
     The barcode reader window  443  is heated to prevent external and internal condensation. The electrical resistance of the heating element is, e.g., between 30-100 Ohms. The barcode reader heated  443  window operates whenever reagent storage  58  is refrigerated. The control algorithm is a simple open loop that modulates the drive current to window  443  to match the resistance of the window and the ambient temperature. 
     5.3.5.5 Reagent Carousel and Kits 
     Referring to the embodiment depicted in  FIGS. 28A-C , prior to use, both the bead and conjugate reagents are stored in packs  80  contained within reagent carousel  70 . Reagent carousel  70  is removable and has slots  465  for holding up to twenty or more reagent packs  80 . Each pack  80  has capacity for up to four bottles  82 , e.g., 2 bead bottles and 2 conjugate bottles. In some cases, diluent or other reagent fluids may be provided. Whether each bottle gets used in a particular pack is chemistry dependent. All reagent packs are identifiable, e.g., barcoded  472 , preferably during the manufacturing process. Barcode  472  includes information such as reagent type, bead lot, expiration date, etc.; Barcode  472  is preferably located on the outer end of reagent pack  80  enabling identification after it is inserted into one of slots  456  of carousel  70 . 
     To limit reagent and conjugate evaporation as well as preventing dust and other particles entering the bottles, the reagent pack  80  (also termed reagent kit or reagent cartridge) design incorporates two levels of seals. A primary foil seal covering each bottle is used to prevent spillage and evaporation during shipping and prior to use. A secondary seal, or flip top lid  470  covers all reagent bottles  82  in pack. The lid can be connected to a pushrod mechanism inside the individual reagent pack  80  and spring loaded in the closed position as shown in  FIG. 28A . As the pack lid opener pushes down on the pushrod as described below, lid  470  is forced open on this individual pack. 
     Examples of a bead reagent bottles are shown in  FIGS. 28B and 28C . Reagent bottles  82  include an access hole at top of bottle  82  to allow reagent transfer robot  60  access. A lip  461  on top edge serves as an attachment point for foil sealing which covers hole  460  until reagent is ready for use, at with time foil seal is pierced by pack piercer  420 . A vertical rib  462  on the side of bottle  82  promotes vertical mixing of the bead suspension. Without such rib  462  or other mechanism, significant vertical gradients in bead concentration may exist even with high levels of agitation. Radial ribs  464  across bottom of bottle  82  engage planetary gear heads  453  to facilitate agitation when the beads have settled out of suspension. A circumferential rib  469  on bottom helps centralize bottle  82  on planetary gear heads  453 . A relatively conical or tapered bottom  466  helps minimize dead volume. During storage outside of the instrument  10  or transportation the beads may settle out of suspension and typically concentrate in the lowest point in the bead bottle, which in this case is an approximately flat bottom, e.g., approximately 6 mm in diameter, to distribute settled beads. Other versions of the bead bottle have a conical center, however, when the beads settled they may form a tight clump in the center of the bottle and may be difficult to re-suspend. With a flat portion  468  on the bottom, settled beads form a thin film across the entire flat surface instead of clumping and may require less agitation during re-suspension. 
     Reagent pack  80 , also termed reagent kit or cartridge, can be stored on the instrument once opened, and includes the appropriate reagents to carry out sample testing, wash solution is typically, although not necessarily supplied separately by the system fluidics. In one embodiment, each reagent kit includes one bottle of sample diluent, one bottle of coated magnetic beads, and one bottle of conjugate as shown in  FIG. 28A . Preferably, pack  80  includes enough reagent material to carry out a large number of tests, e.g., 100 tests. 
     Reagent kits  80  may contain reagents including beads that allow the end user to control and monitor the quality of results for each individual sample. For example, two specific bead “regions” may be used. First, in order to ensure an appropriate sample has been added to the reaction, the M.A.D. system chemistry can employ a bead called “Serum Verification Bead.” This bead ensures that either serum or plasma was used in the assay, and that the appropriate volume of sample has been added to the reaction. If samples other than serum or plasma (i.e., urine, cerebral spinal fluid, nasal aspirates etc.) are used in the assay, or if the incorrect volume of sample is added to the reaction vessel, the Serum Verification Bead will identify a possible issue, and flag the results. Second, in order to ensure consistency of reading by the lasers within detector  20 , the system chemistry can employ a bead called “Internal Standard Bead.” This bead adjusts for variable laser detector response, standardizing the laser for each read. 
     Reagent carousel  70  also provides an interface between the reagent bottles and the agitation gears  453 . Agitation of each reagent bottle  82  about its vertical axis assists to maintain bead homogeneity within the reagents. As described above, reagent storage  58  design rotates individual reagent bottles with an oscillatory motion to achieve consistent homogeneity. The bottle design includes a vertical rib to promote mixing both radially and vertically within the bead suspension. As shown in  FIG. 26 , each Reagent Pack contains 2 bead bottles, which are agitated by rotating each container about its vertical axis. 
     Reagent temperature sensors may be used to monitor the temperature of the reagent storage  58 . Reagent storage  58  utilizes thermistors temperature sensors, for example two sets of two sensors. One set of thermistors, referred to as air sensors, measure the air temperature within the reagent cooler  410 . These sensors provide the primary feedback for the temperature control algorithm. The second set, referred to as the wall sensors, measure the temperature of the evaporator wall. The feedback from these sensors is used to prevent excessive refrigeration of the evaporator and potential icing problems. Redundant temperature sensors are used to assist in troubleshooting during service and maintenance. 
     5.3.5.6 Pack Piercer 
     Referring to  FIGS. 29A-29C , reagent pack piercer  420  is a sub-system within the reagent storage assembly  58  of the MAD instrument  10 . Reagent pack piercer  420  is used to open the primary seal on each reagent bottles  82  in a pack  80  just prior to the first reagent aspiration from that reagent pack  80 . Once opened, the primary seal cannot be closed. The secondary seal, or reagent pack lid  470 , is used to prevent evaporation after the primary seal is opened. 
     Reagent pack piercer  420 , located on reagent cooler lid  412 , includes a drive mechanism  446  attached to the rear of the reagent storage and a piercer arm  421  which extends over the reagent cooler  410  to actuate a number of piercer pins  480 , in this case four as reagent packs  80  in this example are designed to hold up to four reagent bottles  82 . Piercer arm  421  also supports the reagent storage insulation lid  412  and reagent pack lid opener mechanism  430 . The reagent pack piercer  420  is used to open the primary seals on reagent bottles  82  prior to the first reagent aspiration from the reagent pack  80 . The primary pack seals are opened by driving the piercer pins  480  down through the sealing foil and to create a set of holes that match the diameter of the piercer pin tips  481  (see  FIG. 31A-C ). The piercer pins  480  are then retracted so reagent can be aspirated from the reagent pack. 
     In this embodiment, pack piercer  420  and the reagent cooler lid  412  use the same motor  446 . Pack piercer  420  uses the motor only when lid  412  is in the closed position. Once the lid is closed, the motor drives the lever arm  421 , with piercers  480 ,  481  at the end, down into the reagent packs  80 . 
     Drive mechanism  446  preferably, although not necessarily includes the following features. A ball screw drive is used to prevent high friction forces variations due the high working loads. A belt drive is used due to the space constraints and to provide easier service access to the motor. Lead nut is free to float within the retainer so that side loads do not cause excessive wear or degradation to the bearings within the nut. All side loads are carried by two sealed bearings on the lower ends of the drive links. A spherical bearing connects the drive links to the piercer arm  421  to prevent possible binding caused by over constraining the mechanism. 
     A number of sensors or detectors are association with pack piercer  420 . For example, a pack piercer home optical sensor located on piercer arm  421  determines the home position of pack piercer  420  from which the piercers  480  can lower into the reagent packs  82 . 
     A pack piercer/lid step optical sensor determines if step-loss is occurring during either pack piercing or lid movement (raising or lowering). This sensor is located on the rotational gearing used to pierce and move the lid. 
     The pack piercer also uses an optical sensor to detect the position where the insulation lid seals against the evaporator top edge. The design was chosen because it eliminates any problems due to backlash in the reagent lid system. 
     An optional lid closed sensor  482  using a flag  485  that breaks optical sensor  482  (e.g., see  FIG. 31A ) serves as a collision detection sensor during the lid lower action. If the lid is obstructed during the lower move the lid will move relative to the piercer arm, the closed sensor is used to flag the collision notifying the software to halt the axis and prompt the user to remove the obstruction. 
     A pack detector mechanism detects the top of the reagent pack during the pierce stroke. This design uses a spring-loaded pin with a flag  485  that breaks an optical sensor  484 . This particular design helps avoid problems due to variation in pack height or backlash in the pack piercer mechanism. 
     A pierce detector flag  492  and sensor  494  mechanism checks the height of each of the piercer pins at the completion of the pierce stroke, e.g., an elevated pin  480  indicates that the pierce has been incomplete. Because each of the piercer pins is spring loaded, the height of the highest pin is measure via the pierce detector&#39;s spring-loaded plate  492  and an optical sensor  494 . 
     A piercer interlock  486  located on the main arm  421  helps prevent piercer probe tips from being exposed while the reagent storage lid  412  is raised. 
     A mechanical clutch  488 , shown in  FIG. 30 , is optionally included as the drive mechanism may be sufficiently highly geared that a user is unable to back drive the mechanism even if power is not applied to the stepper motor. To prevent operators damaging themselves or the instrument  10 , clutch  488  is monitored by a sensor  489 . Disengaging the clutch will cause the instrument  10  to Estop. 
     To ensure alignment to reagent carousel  70 , pack piercer  420  optionally utilizes a floating guide block on the piercer tips  481 . During initial part of the pierce stroke the floating guide block locates onto the carousel top and centers the piercer pins over the reagent bottles. In one embodiment, guide block can tolerate a +/−2.0 mm or more of misalignment between the piercer mechanism and the reagent carousel. 
       FIGS. 31A-31C  depict a typical operation of pack piercer  420  after piercer is initialized during instrument startup, leaving the reagent lid  412  in the closed position. Prior to the first reagent aspiration from a pack  80  (e.g., 3 to 10 seconds, preferably approximately 6 seconds), reagent carousel  70  is rotated to position the reagent pack  80  directly under the piercer pins  480 . Once in position, the pierce probes  481  are driven down. The spring loaded lid actuation pin opens the secondary seal  470  on the reagent pack  80 . 
     The piercer pin guide block  490  engages the reagent carousel and centers the piercer pins  480  over the reagent bottles  82 . The pack detection pin touches the top of the reagent pack, trips the optical sensor  484  and sets the pierce depth to which to drive. As the probe tip  481  drives down, the piercer probe tip shoulders  483  bottom out on the bottle tops as shown in  FIG. 31C . 
     Spring loading on each pin  80  takes up the difference in bottle heights while the piercer  481  tip travels to the full pierce depth. At the pierce depth the pierce detection optical sensor  494  senses whether all piercer pins have successfully pierced the pack. After successfully piercing the bottles  82 , the piercer pins are retracted and the reagent lid  470  is returned to the closed position. 
     As mentioned above, pack piercer  420  is also used to open and close the reagent storage lid  412 . During a typical open and close procedure, reagent storage insulation lid  412  is closed and held down by gravity. To open the lid, piercer  420  lifts the reagent storage insulation lid to the point where it engages on the underside of the external cover. The piercer continues to lift, raising the external cover to a point where a pulley on the front of the piercer engages in a slot on the external cover. As the piercer continues to lift, the external cover reaches a point where the gas strut overcomes the weight of the cover. The piercer is now required to hold the external cover down. When piercer reaches the top of its travel, lid is fully open and reagent carousel can be raised. To lower the lid the same steps are repeated in reverse. 
     5.3.5.7 Reagent Pack Lid Opener 
       FIG. 32  depicts a reagent pack lid opener assembly  430 . Lid opener  430  is a sub-assembly within the reagent storage assembly  58  of the MAD system  10 . Reagent pack lid opener  430  opens and closes the secondary seal (e.g., reagent pack lid  470 ) on a reagent pack  80  just prior to aspiration of a reagent. To minimize reagent evaporation reagent pack lid opener  430  does not open the secondary seal on other reagent packs  80 , which are not required for that particular reagent aspiration process. 
     Reagent pack lid opener  430  preferably performs up to 3 or more lid open and close operations per test. In one example, based on 800 tests per day, 365 days per for 7 years, this equates to over 6,000,000 cycles. 
     Reagent pack lid opener  430  is designed to minimize the amount it encroaches on the reagent storage lid  412  insulation. In one example, a lid insulation thickness of approximately 15 mm assists in minimizing or preventing condensation forming on the outside of the lid when the instrument is operating at high end of the temperature and humidity range. 
     Reagent pack lid opener  430  optionally has a low profile to prevent clashing with the reagent transfer robot  60  during aspiration (e.g., see  FIG. 25 ). The underside of the reagent transfer robot, at the bottom of its vertical travel in each of the four aspiration positions, defines the top of the operating space envelope. 
     Reagent pack lid opener  430  is aligned to reagent pack piercer mechanism using a hole and slot with 2 dowel pins. As the pack piercer  420  is aligned to the Reagent Carousel using a jig, the lid opener  430  mechanism inherits the same alignment. 
     To provide the maximum alignment tolerance between the reagent carousel  70  and lid opener mechanism  430 , the design uses large diameter buttons  512  in the reagent carousel  70  and smaller actuation pins  500  in the lid opener. The lid opening buttons in the reagent carousel provide accurate alignment with the lid  470  hinge on each reagent pack  80  and a large target area for the actuation pins  500 . 
     During the “open pack lid” action the reagent pack opener gearing  508 , including a smaller gear  514  attached to stepper motor  510  and a larger gear that drives pin actuation arm  501 , overdrives the vertical axis to ensure packs lids are always opened fully. Larger gear  512  in the vertical drive is spring  504  loaded to prevent steploss. This permits the stepper motor  510  to drive through the full range of movement regardless of where the carousel  70  is positioned, within the 2.0 mm vertical tolerance zone. 
     In one embodiment, no direct steploss detection is used on the reagent pack lid opener  430 . In the case of steploss on either the horizontal or vertical axis during the lid opening process will, at worst, cause the reagent transfer robot  60  to steploss on its descent into the reagent pack  80 . While the initial steploss is not detected, respective home optical sensors, e.g., vertical (rotational) home sensor  506  and horizontal home sensor  502 , will sense that steploss has taken place on the vertical axis when actuation finger  501  is raised to close the pack lid; or on the horizontal axis when finger  501  prepares to open well  500   a.    
     As shown in  FIG. 32  reagent pack lid opener includes an actuation mechanism  499  attached to the top of the reagent storage lid  412  and actuation pins  500   a - 500   d  which are used to transfer the actuation force through lid  412  to the top of the reagent carousel  70 . Actuation pins  500   a - 500   d  (generally termed actuation pin  500 ) are located to align with the reagent pack  80  lid above the aspiration points for each of, in this case, four reagent bottles. Lid opener  430  uses a finger  501  to depress the actuation pins  500   a - d  and utilizes a spring, e.g.,  505   d  or similar mechanism for each pin  500  to return to the raised position. Finger  501  has a horizontal axis  503 , which permits finger  501  to travel between the four actuation pins  500 . 
     In one example of typical operation, the pack lid opener  430  is initialized during instrument startup. Approximately 3 seconds prior to a reagent aspiration, finger  501  is moved to position it above the required actuation pin, e.g.,  500   a . This action is called “Prepare to open pack lid”. Just prior to a reagent aspiration, finger  501  is rotated down, the actuation pin  500   a  engages the reagent carousel  70  and the reagent pack lid  470  is opened. This action is called “Open pack lid”. The reagent robot then lowers reagent probe  61  into the reagent pack  80 , reagent is aspirated and reagent probe  61  is extracted. Finger  501  is rotated to a raised position and spring  505  force returns the actuation pin  500  to the raised position. This action is called “Close pack lid”. 
     5.3.5.8 Typical Operation of Reagent Storage Assembly 
       FIG. 27  depicts a typical operation of reagent storage assembly  58 . Briefly, the reagent storage  58  lifts the lid and raises the lifting platen  455  to the reagent carousel  70  installation position. Lifting platen  455  then rotates to present the desired reagent pack location to the user. The user installs either a new pack or replaces the entire reagent carousel  70 . Reagent storage  58  lowers lifting platen  455  and closes the lid  412 . Barcodes  472  are read to identify any new reagent packs  80 . 
     Reagent storage  58  agitates the reagent pack for a period of time, e.g., four minutes, and reagent packs are ready for use. The reagent packs are periodically agitated to ensure uniform bead density throughout each bottle  82 . 
     If the instrument  10  requires a specific reagent (in this case, from a new pack), the new reagent pack is rotated to a pack piercing position below pack piercer  420 . Pack piercer  420  then moves down, opens the reagent pack lid, and breaks the primary seal on all of the reagent and conjugate bottles within the pack. Pack piercer  420  returns to the ready position allowing reagent pack lid  470  to close. Reagent pack  80  is rotated to the proper aspiration position (based on which reagent or conjugate bottle is to be aspirated from). Pack lid opener  430  opens the reagent pack lid  470 . Reagent probe robot  60  aspirates the desired amount of reagent or conjugate. Pack lid opener  430  then closes the reagent pack lid  470 . 
     5.3.5.9 Example Specifications of Reagent Storage Assembly components 
     The following TABLES 2-12 provide specifications for various reagent storage assembly  58  components described above. The specifications and values provided in the table are intended only as examples according to one embodiment, and are in no way limiting of the scope of the invention. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Sample materials each of the reagent storage assembly gears 
               
            
           
           
               
               
               
            
               
                   
                 Gear 
                 Material 
               
               
                   
                   
               
               
                   
                 Sun gear 
                 Acetyl 
               
               
                   
                 Planetary gear hub 
                 Lubriloy D 
               
               
                   
                 Inner planetary gear 
                 Polyurethane (95 shoreA) 
               
               
                   
                 Outer planetary gear 
                 Nylon (6,6) 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 details the drive ratios for the agitation and turntable axes. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                 Secondary 
                   
                   
               
               
                   
                 Stepper Pulley 
                 Pulley 
                 Degrees 
                 Steps per 
               
               
                 Axis 
                 (No. of teeth) 
                 (No. of teeth) 
                 per step 
                 degree 
               
               
                   
               
               
                 Agitation 
                 24 
                 192 
                 0.225 
                 4.4444 
               
               
                 Turntable 
                 24 
                 192 
                 0.225 
                 4.4444 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 details the drive ratios for the carousel lifter and agitation 
               
               
                 drive. 
               
            
           
           
               
               
               
            
               
                   
                 Axis 
                 Drive ratio 
               
               
                   
                   
               
               
                   
                 Lead screw pitch 
                 25 mm/rev 
               
               
                   
                 Agitation gear ratio 
                 212:28 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Suggested agitation parameters 
               
            
           
           
               
               
               
               
            
               
                 Agitation 
                 Amplitude 
                 Frequency 
                 Period 
               
               
                   
               
               
                 New pack 
                 450 degrees of rotation 
                 1.5 Hz 
                  4 minutes on 
               
               
                 introduction 
                 at the bead bottle 
               
               
                 Steady state running 
                 450 degrees of rotation 
                 1.5 Hz 
                  3 seconds on 
               
               
                   
                 at the bead bottle 
                   
                 12 seconds off 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Suggested nominal distances between hardware elements. 
               
            
           
           
               
               
            
               
                 Angular displacement 
                 Default Angle 
               
               
                   
               
            
           
           
               
               
               
            
               
                 Carousel checking pin 1 - from lifting platen vertical 
                 32 
                 deg CW 
               
               
                 home pin 
               
               
                 Carousel checking pin 2 - from lifting platen vertical 
                 122 
                 deg CW 
               
               
                 home pin 
               
               
                 Carousel checking pin 3 - from lifting platen vertical 
                 212 
                 deg CW 
               
               
                 home pin 
               
               
                 Carousel checking pin 4 - from lifting platen vertical 
                 302 
                 deg CW 
               
               
                 home pin 
               
               
                 Agitation drive slot length 
                 144 
                 deg 
               
               
                 Lifting platen lowered (drive pins at end of drive 
                 300 
                 deg ACW 
               
               
                 slots) - Dog clutches disengaged 
               
               
                 Agitation drive pin centred in slot - Agitation drive pin 
                 72 
                 deg 
               
               
                 at end of drive slot 
               
               
                 Maximum lifter travel (rotational) 
                 1656 
                 deg 
               
            
           
           
               
               
            
               
                 Maximum lifter travel (distance) 
                 mm 
               
            
           
           
               
               
               
            
               
                 Stopping distance on proximity sensor - equivalent 
                 5 
                 deg 
               
               
                 to 0.35 mm vertical 
               
               
                 Back off distance for proximity sensor 
                 72 
                 deg 
               
               
                 Stopping distance on back off from proximity sensor 
                 10 
                 deg 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Suggested nominal drive currents for drive motors. 
               
            
           
           
               
               
            
               
                 Motor duty 
                 Current 
               
               
                   
               
            
           
           
               
               
               
            
               
                 High hold current - 
                 1 
                 amp 
               
               
                 used by turntable motor during agitation and carousel 
               
               
                 raise and lower 
               
               
                 Low hold current - 
                 0.5 
                 amps 
               
               
                 used by turntable and agitation motor while stationary 
               
               
                 Agitation current - 
                 6 
                 amps 
               
               
                 used by agitation motor during agitation 
               
               
                 Move current - 
                 4 
                 amps 
               
               
                 used by turntable and agitation motor during carousel 
               
               
                 rotation 
               
               
                 Acceleration and deceleration current - 
                 6 
                 amps 
               
               
                 used by turntable and agitation motor during carousel 
               
               
                 rotation 
               
               
                 Lower carousel move current - 
                 1 
                 amp 
               
               
                 used by agitation motor during carousel lower (the low 
               
               
                 current eliminates the danger of crushing users fingers) 
               
               
                 Lower carousel acceleration and deceleration current - 
                 1.5 
                 amps 
               
               
                 used by agitation motor during carousel lower (the low 
               
               
                 current eliminates the danger of crushing users fingers) 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 Suggested acceleration and velocities for the hardware elements. 
               
            
           
           
               
               
               
            
               
                   
                 Parameter 
                 Default Value 
               
               
                   
                   
               
               
                   
                 Disengage and engage dog clutch velocity 
                  45 deg/sec 
               
               
                   
                 Raise and lower lifting platen acceleration 
                 1000 deg/sec 2   
               
               
                   
                 Raise and lower lifting platen velocity 
                  450 deg/sec 
               
               
                   
                 Vertical home velocity 
                  100 deg/sec 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 9 
               
             
            
               
                   
               
               
                 Suggested default soft set-ups for the turntable and agitation drive. 
               
            
           
           
               
               
            
               
                 Position - Relative to home 
                   
               
               
                 Home = 154.1 clockwise from the front centre 
                 Default Distance 
               
               
                   
               
            
           
           
               
               
               
            
               
                 Lifting Platen vertical home pin 
                 30.4 
                 CW 
               
               
                 Lifting platen lowered (drive pins at end 
                 1440 
                 deg CW 
               
               
                 of drive slots) - Lifting platen raised 
               
               
                 Pack 1 - Outer Bead Bottle Aspirate Position 
                 56.5 
                 CCW 
               
               
                 Pack 1 - Inner Bead Bottle Aspirate Position 
                 51.4 
                 CCW 
               
               
                 Pack 1 - Outer Conjugate Bottle Aspirate Position 
                 43.2 
                 CCW 
               
               
                 Pack 1 - Inner Conjugate Bottle Aspirate Position 
                 30.8 
                 CCW 
               
               
                 Pack 1 - Barcode 1 Read Position 
                 80.9 
                 CW 
               
               
                 Pack 1 - Barcode 2 Read Position 
                 80.9 
                 CW 
               
               
                 Pack 1 - Pierce Position 
                 115.9 
                 CW 
               
               
                 Pack 1 - User Access Position 
                 154.1 
                 CCW 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 10 
               
             
            
               
                   
               
               
                 Suggested reagent bottle nominal positions 
               
            
           
           
               
               
               
            
               
                   
                 Position 
                 Distance from rotational axis 
               
               
                   
                   
               
               
                   
                 Well 1 (Outer bead bottle) 
                 148.45 mm 
               
               
                   
                 Well 2 (Inner bead bottle) 
                 120.15 mm 
               
               
                   
                 Well 3 (Outer conjugate bottle) 
                 100.45 mm 
               
               
                   
                 Well 4 (Inner conjugate bottle) 
                  87.55 mm 
               
               
                   
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 11 
               
             
            
               
                   
               
               
                 Suggested nominal vertical heights of the reagent storage elements 
               
            
           
           
               
               
               
            
               
                   
                 Interfacing element 
                 Distance above Base Support 
               
               
                   
                   
               
               
                   
                 Top of evaporator wall 
                 171 mm 
               
               
                   
                 Top of lid under reagent probe 
                 188 mm 
               
               
                   
                 Base of reagent bottles 
                 90.55 mm   
               
               
                   
                 Top of reagent bottles 
               
               
                   
                   
               
            
           
         
       
     
                     TABLE 12                  Suggested drive ratios for sample stepper motors.                             Axis - position   Drive pulley   Steps/mm   mm/Step                                     Lead screw   Lead screw 2 mm/rev   100   0.01       Piercer tips   ~7 times the lever ratio of the   14   0.0714           ball screw                    
5.3.6 Reagent Robot and Probe Assembly
 
       FIGS. 33-35  show a reagent robot and probe assembly  60 , also referred to simply as reagent robot  60  or reagent transfer assembly  60 , according to an embodiment of the present invention. Reagent robot  60  generally includes a probe arm and head assembly  520  for mounting a reagent probe  61  similar to aspiration probe  370  described above, a rotational motor assembly  522 , a vertical column and motor assembly  524 , a base  526 , a power in and rotational circuit board (PCB)  528 , a vertical movement PCB  534 , and a liquid level sense PCB  536 . Reagent robot  60  accurately aspirates reagent and conjugate from reagent storage  58  and dispenses the reagent and/or conjugate into reaction vessels in incubator carousel  57 . The reagent robot further provides liquid level sensing for use in tracking reagent usage. During use, the reagent robot moves to “stow” position when reagent storage assembly  58  is opened and pauses operation. Furthermore, reagent robot  60  cleans the reagent probe  61  in a wash station similar to aspiration wash station  90  to prevent any material carryover and/or contamination. 
     Probe  61  (shown with reagent robot  60  in  FIG. 25 ) is threaded into probe head  521  (also termed probe mount  521 ). Reagent probe  61  transfers reagents from the reagent storage  58  to RVs on the incubator carousel  57 . In the present embodiment, reagent probe includes the same features as, and is interchangeable with, specimen probe  370  described above with respect to  FIGS. 22 and 23 . For example, the tip of probe  61  has a reduced internal diameter to increase fluid dispense velocity and aid dispense accuracy. Top of probe  61  is preferably connected near probe mount  521  to a reagent syringe pump (e.g., a Cavro XP3000 syringe pump or the like) by a length of rigid walled PTFE or similar tubing filled with buffer fluid. 
     Probe arm and head assembly  520  includes probe mount  521 , the connection to the reagent syringe pump and a probe blockage sensor, or pressure transducer. Arm  520  (and therefore, the probe) is adjusted horizontally by using the slotted screws  523  attaching arm  520  to the vertical column  525 . As shown in  FIG. 34 , this adjustment provides the radial alignment required to align the probe for accurate movement between clean station  527 , reagent storage  58  (e.g., four positions such as access ports  530   a - d ), and incubator carousel assembly  56  (e.g., two positions such as access ports  532   a  and  532   b ). 
     Head  521  provides a connection for the fluidics tubing and the liquid level sensing  536  to the reagent probe  61 . Probe  61  is preferably threaded into the underside of head  521  with a small o-ring providing a seal. Head  521  provides adjustment of the probe in the z-angular direction relative to the probe head. The adjustment is in the x-y directions of the probe head only. Essentially, this moves the probe tip in either the x-y directions while the probe base (threaded into the probe head) is stationary. 
     A pressure transducer can be used to detect partial or complete blockages of the probe. The instrument monitors the pressure transducer for pressures outside the range of normal operation. Pressures outside of the normal operating range can be due to a number of factors. Error codes for each out of range pressure exist and assist with troubleshooting. The liquid level sensor  536 , probe mount  521 , reagent probe  61  and tubing are optionally interchangeable with those used on specimen handler assembly  66 . 
     Rotational motor assembly  522  drives a belt and gear  527  to rotate vertical column  525  and thus reagent probe arm  520  through a fixed arc as shown in  FIG. 34 . Hard stops are located at the end of the travel arc. During normal operation, the travel arc is from incubator carousel assembly  56  middle ring, corresponding to port  532   b , to the reagent carousel inner hole  530   d . Clean station  527  is also included (approximately at the center) in the arc of motion. 
     The rotational home position of the probe preferably does not correspond to clean station  527  center. This design allows the reagent robot  60  clean position to be adjusted rotationally using motor assembly  522  to turn vertical column  525 . 
     Vertical column and motor assembly  524  moves the reagent arm  520  and probe  61  in the vertical direction. The amount of travel is governed by different parameters for each specific location (e.g., incubator carousel  57 , clean station  527 , and reagent storage  58 ). The vertical travel at the incubator carousel  57  and clean station  527  is set to a fixed position determined during instrument alignment procedures. Liquid level sensor  536  determines the vertical travel at the reagent storage  58 . Each parameter can be modified using a service program interface within the MAD host  40  software. The vertical movement is accomplished using motor  524  which employs a belt and gear system to move the top portion  538  of the vertical column  525  up and down. Additionally, a spring  529  is used to help hold column  538  in the up position when holding current is removed from the motor. Essentially, this prevents the probe from becoming damaged by collision with other parts when the instrument power is turned off. 
     Base  526  is mounted to the instrument SPM  30  chassis by two or more bolts, and provides a stable platform on which all other reagent robot  60  components are mounted. Base  526  also incorporates hard range of motion stops that physically prevent reagent robot  60  from moving outside the defined range of motion. 
     Example characteristics of vertical axis  524  and theta axis  522  stepper motors that may be employed in reagent robot  60  are shown in tables 13 and 14, respectively. In both examples below, stepper motors for the vertical  524  and theta  522  axis are attached to a pre-tensioned belt, which is attached to the vertical arm  525  of reagent robot  60 . 
     
       
         
           
               
             
               
                 TABLE 13 
               
             
            
               
                   
               
               
                 Example characteristics of a vertical axis stepper motor 
               
            
           
           
               
               
               
               
            
               
                   
                 Feature 
                 Number 
                 Comment 
               
               
                   
                   
               
               
                   
                 Resolution of stepper 
                 200 steps per turn 
                 Full stepping 
               
               
                   
                 PCD of pulley 
                 11.2 mm 
                 14 tooth pinion 
               
               
                   
                 Resolution on the Axis 
                 0.17584 mm/step 
               
               
                   
                   
               
            
           
         
       
     
                     TABLE 14                  Example characteristics of a theta axis stepper motor                         Feature   Number   Comment               Drive ratio   5.714285714   14 tooth pinion and               80 tooth gear       Resolution of stepper   1600 micro steps   200 step per turn with           per rev   8 micro steps per full step       Radius of point on Axis   168 mm   Probe arm radius       Resolution on the Axis   0.115395 mm       Resolution on the Axis   0.039375 degrees   0.039375                    
5.3.6.1 Reagent Robot Circuit Boards and Sensors
 
     Referring to  FIG. 35 , power in and rotational printed circuit board (PCB)  528  provides a single electrical connection to the instrument via backplane  200 , operational power and sensing to horizontal, or rotational, motor  522 , and operational voltages (drive &amp; sensing voltages) to all other reagent robot  60  components. The input signals from the instrument are received via a large ribbon cable attached to the PCB. The operational power and sensing for the rotational motor  522  is distributed to the motor and optical sensor  540  by two wire connections to the PCB. The remaining operational voltages (for the rest of reagent robot  60  components) are transferred via a single cable to the vertical movement PCB  534 . Rotational step optical sensor  540  determines the rotational position of the Reagent Robot and provides step loss monitoring. The sensor is located on the rotational drive motor assembly  522 . A rotational home optical sensor (not separately shown) preferably determines the rotational home position of reagent robot  60 . This sensor is located on the power in and rotational PCB  528 . If replacement is required, the entire PCB is replaced. PCB  528  in this embodiment is located on a bracket that is directly mounted to base  526  as shown in  FIG. 33 . 
     Vertical movement PCB  534  provides power and sensing to the vertical motor  524  and power to the liquid level sense PCB  536 . The operational power and sensing for vertical motor  524  is distributed to motor  524  and optical sensor  542  by two wire connections to PCB  534 . Liquid level sense PCB  536  is connected via a ribbon cable. Vertical movement PCB  534  is mounted on the non-moving portion of vertical column  525 . Vertical step optical sensor  542  determines the vertical position of reagent robot  60  and provides step loss monitoring. This sensor  542  is located on vertical drive motor assembly  524  and is connected to the vertical movement PCB  534 . Vertical home optical sensor (not separately shown) is located on PCB  534  and determines the vertical home position of the robot  60 . If replacement of this sensor is required, the entire PCB is replaced. 
     Liquid level sense PCB  536  uses capacitance sensing to determine when the probe comes into contact with a liquid. The instrument uses this information to determine the probe insertion depth into the reagent pack and reagent volume remaining within the bottle. Liquid level sense PCB  536  is mounted on the moving portion  538  of the vertical column  525 . Additionally, a ground lug from the reagent storage assembly  58  is attached to the reagent robot to ensure proper operation of liquid level sensor  536 . 
     5.3.6.2 Operation of Reagent Robot 
     In an example of typical operation of reagent robot  60 , probe  61  is cleaned at the clean station  527 . Reagent robot  60  returns to the ready position over clean station  527 . Reagent robot  60  then rotates probe  61  over a specific well, e.g., port  530   a , in reagent storage  58 . Reagent robot  60  then lowers the probe into the reagent pack and aspirates a specific volume of reagent. After aspiration, reagent robot  60  lifts the probe above the reagent storage assembly  58  and rotates over the incubator carousel  57 . Once over the proper location of incubator carousel  57 , robot  60  lowers probe  61  into a hole, e.g.,  532   a , in the incubator carousel  57  lid. Reagent robot  60  then dispenses the reagent into an RV on the incubator carousel  57 . After dispensing reagent, the reagent robot  60  raises the probe from incubator carousel  57  and rotates probe  61  to the center of the clean station  527 . Finally, reagent robot lowers probe  61  into the clean station  527  for cleaning 
     5.3.7 Incubator and Separation Carousel Assembly 
     5.3.7.1 Overview of Incubator and Separation Carousel Assembly 
       FIGS. 36-42  depict the structure and function of an incubator and separation carousel assembly  56  (also generally referred to herein as “incubator carousel assembly” 56) according to an embodiment of the present invention. Referring to  FIG. 36 , the incubator and separation carousel assembly  56  is designed to incubate the reaction vessels at predetermined temperatures. Preferably, assembly  56  incubates specimens at not less than about 34° C. and not more than about 39° C. with a stability of about ±0.5° C. over an interval of about 45 minutes. The assembly  56  also agitates the reaction vessel during incubation at defined intervals for approximately about forty percent of the incubation period. Preferably, the agitation frequency is about 22 Hertz with an amplitude (peak to peak) of about six millimeters for about three seconds. Of course, other incubation and/or agitation parameters may appropriate for a given assay and be used without departing from the scope of this invention. The outer separation carousel  55  portion of incubator carousel assembly  56  also magnetically holds the beads (described below) in reaction vessels when liquid contained in the reaction vessel is aspirated. Preferably, each reaction vessel located on separation carousel  55  is associated with two magnets, positioned to maximize bead retention as described in more detail below. Incubator and separation carousel  56  also moves the reaction vessels to defined positions for aspiration, dispense, and movement. It is preferred that the time required to move any reaction vessel to another location is less than about 0.5 sec. 
     Incubator and separation carousel assembly  56  interfaces with other sub-modules and components of system  10 , e.g., as shown below in TABLE 15. 
     
       
         
           
               
             
               
                 TABLE 15 
               
             
            
               
                   
               
               
                 Incubator And Separation Carousel Assembly Interactions* 
               
            
           
           
               
               
            
               
                 Incubator Carousel interfaces with; 
                 Separation Carousel interfaces with 
               
               
                   
               
               
                 RV Handler 52a 
                 RV Handler 52a 
               
               
                 RV Handler 52b 
                 RV Handler 52b 
               
               
                 Reagent Transfer Robot 
                 Wash Aspiration Probes 
               
               
                 Specimen Transfer Robot 
                 Wash Dispense Probe 
               
               
                   
               
               
                 *Both Carousels interface with RV Handler 1 and RV Handler 2, however they typically do so in different locations. 
               
            
           
         
       
     
     Referring to  FIG. 36  the incubator and separation carousel assembly  56  has a number of components, including, e.g., an incubator lid  550 , an inner incubator carousel  57 , an outer separation carousel  55 , a separation carousel drive  552 , an incubator carousel drive  554 , a tub-incubator chamber  556 ,  558 , and a fan and heater assembly  560 ,  561 . Typically, all of the components are mounted on or attached, directly or indirectly, to a main support casting  562 , that is attached to the main instrument  10  chassis. 
     Incubator lid  550  is insulated to maximize thermal performance and to minimize heat loss. A single large knurled nut  551 , located in the lid center, is used for removal and replacement of lid  550 . Holes in lid  551  allow the RV handlers (e.g. holes  554 ), reagent transfer robot  60 , wash robot  62 , and specimen aspirate robot  66  to access RVs located on either incubator carousel  57  or separation carousel  55 . 
     5.3.7.2 Incubator Carousel 
     Incubator carousel  57  holds a large number, e.g., 100, RVs within two outer rings  57   a ,  57   b  of forty RV receptacles each and one inner ring  57   c  of twenty RVs. Outer two rings  57   a,b  are used for incubating samples while the inner ring  57   c  is used as RV storage only when “temporary” situations occur. For example, a temporary storage occurs when instrument  10  is unable to process the RVs to either the detector  20  or the waste  64 . 
     Incubator carousel  57  is agitated at a frequency of, e.g., 22 Hertz with an 6 millimeter amplitude (peak to peak) for approximately 3 seconds. Samples are agitated for approximately 29% of the time spent on incubator carousel  57 . Other incubation parameters may be used. 
     TABLE 3 provides and example of which incubator carousel rings interface with the various other components of the instrument. 
     
       
         
           
               
             
               
                 TABLE 16 
               
             
            
               
                   
               
               
                 Incubator Carousel Ring Interfaces 
               
            
           
           
               
               
               
               
            
               
                   
                   
                 Middle 
                   
               
               
                 Interfacing device 
                 Outer ring 57a 
                 ring 57b 
                 Inner ring 57c 
               
               
                   
               
               
                 RV Handler 52a 
                 Yes 
                 Yes 
                 Yes 
               
               
                 RV Handler 52b 
                 Yes 
                 Yes 
                 No 
               
               
                 Specimen transfer robot 
                 Yes 
                 No 
                 No 
               
               
                 Reagent transfer robot 
                 Yes 
                 Yes 
                 No 
               
               
                   
               
            
           
         
       
     
     Referring to the block diagram of  FIG. 37 , temperature sensors  570  and  572  are utilized to monitor the temperature of the incubator carousel  57 . The incubator chamber interior temperature and the ambient incubator chamber  556  housing temperature are monitored using dual thermistor assemblies  570 ,  572  respectively, to provide redundancy. The thermistor assemblies  570 ,  572  are connected to the temperature sensor PCB, mounted inside the incubation chamber  556 , which is covered to prevent fluid spills from damaging the circuit. The temperature sensor PCB  574  is mounted to provide cable connection access from the outside of the incubator tub. 
     5.3.7.3 Separation Carousel 
     Separation carousel  55  holds approximately 40 RVs in a single outer ring on an independently driven carousel (e.g., driven by motor assembly  552 ). Separation carousel  55  runs concentrically around the outside of incubator carousel  57 . Separation carousel  55  has several characteristics differentiating it from the incubator carousel  57 . For example, one differentiating characteristic is a number of magnets  580  (with backing plates  582 ) installed in the inner portion of the separation carousel  55  as shown in  FIG. 38 . Magnets  580  hold the microspheres in the RV (which is held in RV receptacle  584 ) while wash buffer is added and removed as described above with respect to  FIG. 8 . Backing plates  582  provide a secure base for the magnets as well as containing the magnetic field to separation carousel  55 . 
     Additionally, due to the high magnetic strength used, separation carousel  55  optionally has a steel magnetic shield  586  installed between the separation carousel and the incubator carousel. Magnetic shield  586  prevents stray magnetic field from interfering with the chemistries occurring on the incubator carousel  57 . 
     The magnetic separation process is used to allow removal of spent sample and reagent following incubation as well as washing of the beads to remove non-specifically bound sample and conjugate reagent. When a RV is placed into separation carousel  55  magnets  582  attract the beads into a patch on the inner wall of the RV. After a separation period of 30-90 seconds, more preferably 55-65 seconds (dependent on scheduler and timing) the carousel moves the RV under the wash aspirate probes. The probes are driven to the bottom of the RV where they aspirate all the remaining fluid out of the RV without aspirating any of the beads. The attraction of the beads to separation magnets  282  forces the bead patch to remain held to the RV wall. Once all the excess fluid has been removed the aspiration probes are retracted from the RV. Separation carousel  55  positions the RV under the wash dispense probe where wash buffer is dispensed into the RV. The wash buffer flows over the bead patch and removes non-specifically bound analyte and conjugate reagent. The separation and wash process is repeated a number of times as specified by the chemistry protocol. 
     TABLE 17 suggests which instrument components typically interface with separation carousel  55 . 
                     TABLE 17                  Separation Carousel Interfaces                                 Separation           Interfacing device   Carousel                       RV Handler 52a   Yes           RV Handler 52b   Yes           Wash Aspirate Probes   Yes           Wash Dispense Probe   Yes           Specimen transfer robot   No           Reagent transfer robot   No                        
5.3.7.4 Separation Carousel Drive
 
     Referring to  FIG. 39 , separation carousel drive  552  contains a servo-motor  552   a , a pulley  590   a , an encoder ring  592 , tensioning spring  596  and a timing belt  594 . All these components work together to move separation carousel  55  to locations required by the host  40  software to complete various tasks (e.g., RV movement, wash buffer dispense or aspiration). 
     Servomotor  552   a , which is commonly used in reagent storage drives, is well suited to its role of slewing separation carousel  55  back and forth. Pulley  590   a  is sized to maintain proper meshing with timing belt  594 . The pulleys  590   a  and  590   b  on the separation carousel  55  and incubator carousel  57  are preferably similar. 
     Encoder ring  592   a , which is mounted on pulley  59   a , allows the sensor to determine the position of the separation carousel  55 . 
     Tensioning spring  596  maintains a specific tension on timing belt  594  throughout its operational lifetime. This reduces vibration, noise and eliminates problems associated with belt wear. Tensioning spring  596  is mounted to the motor mounting  598  and the instrument chassis. Timing belts  594   a ,  594   b , which are preferably the same or similar for both separation and incubator carousel, is preferably although not necessarily a KEVLAR reinforced polyeruthane continuous timing belt. 
     A separation carousel rotational step optical sensor determines the rotational position of the outer carousel  55 . The sensor is located in the incubator carousel housing  556  on the rotational gear, while the optical flags are located on the bottom of the rotational gear. The optical sensors use quadrature encoders to determine and monitor the position of the carousels. The following describes the operation of the sensors with quadrature encoders. 
     Quadrature encoders associated with quadrature optical sensor circuit board  576  of  FIG. 37  provide feedback to the control software for the carousel drives  552 ,  554 . The quadrature encoders sense the encoder ring  592   a ,  592   b  on each of the carousel pulleys, providing feedback from the carousel side of the drive system and detecting belt breakage or slippage. 
     Each carousel  55 ,  57  has its home position identified by one slot on the step loss detection castellated ring  592   a ,  592   b , which is 150% larger than the other slots. The home position is found by rotating the carousel until both sides of the slot have been detected. The carousel is then driven back to the center of the slot and is considered homed. 
     Both of the carousel motor drives  552 ,  554  in the assembly  56  use a quadrature encoder for position feedback. Two techniques are used to monitor the drive positions during rotations and while static. 
     The basic feedback is provided by an optical quadrature encoder positioned under a slotted ring  592   a ,  592   b  that is incorporated into the web of the large drive pulleys  590   a ,  590   b  on each of the carousel drives. The encoder produces two slightly out of phase signals. The rotational direction of a slot passing between the sensor&#39;s detector and emitter is determined by the order in which the sensor signals change state. 
     The first technique used for tracking the carousel positions uses a high-speed counter to track the total number of slots passed. Slots detected in clockwise direction are added to the total count while slots detected in counter-clockwise direction are subtracted from the total. Due to the speed of the counter the cumulative slot count is capable of tracking slots during fast moves and agitation even where mechanical vibration causes effects similar to switch bounce. The counter output is predominantly used after a carousel move or after agitation to check that the carousels are in the correct position prior to interfacing with another device. 
     The second technique used for position tracking is used to detect loss of position control during moves and agitation. When an error or collision is detected the drive current to the motor is instantly removed in an effort to minimise the possibility of damaging the carousel or the object it has collided with. During a move or agitation the control software calculates the exact time when the encoder will be in the middle of either a slot or the adjoining rib. The software then checks at each calculated time to compare the sensor state to the predicted state. If a discrepancy is detected a position error is reported. 
     5.3.7.5 Incubator Carousel Drive 
     Incubator carousel drive  554  is essentially the same or similar to the separation carousel drive  552  except for the motor and bearing. While the separation carousel drive does not use a bearing, the constant agitation of the incubator carousel  57  benefits from the use of a bearing to provide impact and vibration cushioning. The demands on the incubator carousel motor, slew and agitation, suggest that this motor preferably is more durable and reliable than the motor used in the separation carousel. Additionally, the bearing chosen provides both impact and vibration cushioning and prevention of bearing failure due to localized welding and consequent pitting. 
     Incubator carousel rotational step optical sensor determines the rotational position of the Incubator. The sensor is located in the incubator carousel housing underneath the rotational gear. 
     5.3.7.6 Tub—Incubator Chamber 
     Incubator chamber  556 ,  558  is preferably fabricated from structural polyurethane foam to provide good thermal insulation. The thermal insulation is beneficial to prevent heat flow into the rest of the instrument and to provide a constant air temperature throughout the incubator. The incubator chamber minimizes the heat loss by insulating the casting, minimizing air leakage through the timing belt slots and providing a cover for the wash aspirate and dispense probes. Incubator chamber  556 ,  558  also provides an overflow drain to prevent any liquid from reaching heater  561 . 
     Additionally, mounts for the reagent transfer robot and specimen transfer robot clean stations are preferably located on the incubator chamber. 
     5.3.7.7 Fan and Heater 
     The incubator assembly  56  is heated to provide an optimised stable environment for the assay chemistry. A predefined warm-up time for the incubator is preferable because the incubator is generally only constantly heated during assay chemistry. 
     To avoid adding mass to incubator carousel  57  an air heating element  561  and fan  561  are beneficial to control temperature inside the incubator. Heater  561  and fan  560  are preferably automatically configured to permit either 110/240 volt compatibility when the instrument is configured to the source voltage. 
     A single use thermal fuse protects the heater element from any over-temperature conditions that may occur. The nominal trip temperature for the thermal fuses is 70° C. (˜184° F.). Software will typically flag any thermal fuse trips or defective heater as a temperature out of range condition. 
     Fan  560  is preferably equipped with a tacho output to enable detection of fan failure or error. Fan and heater assembly  560 ,  561  is removed from the bottom of the incubator and separation carousel assembly  56  without requiring the accessing of either carousel. 
     Fan  560  circulates the heated air around below the incubation carousel. Dual thermistors monitor the air temperature  570  and provide feedback to the heater control circuitry  561   a ,  561   b . The air thermistors are mounted on the metal housing surrounding the drive mechanisms. 
     5.3.7.8 Operation of Incubator and Separation Carousel Assembly 
     According to one embodiment, typical operation of incubator and separation carousel assembly  56  is as follows. An RV is removed from the RV supply  262  and delivered to incubator carousel  57  outer ring  57   a  by RV Handler  52   a . Incubator carousel  57  rotates the RV to the reagent dispense position where reagent is added. Incubator carousel then rotates the RV to the sample dispense position where sample is added. Incubator Carousel  57  then agitates and incubates the RV. 
     After agitation and incubation of the sample in the RV, incubator carousel  57  rotates the RV to a RV pickup position where the RV is removed from the incubator carousel placed on separation carousel  55  by RV Handler  52   b . The separation carousel rotates the RV to the wash aspirate probe position where the wash probe robot removes the liquid. Separation carousel  55  rotates the RV to the wash dispense position where liquid is added to the RV. 
     After washing, separation carousel  55  rotates the RV to a RV pickup position where the RV is removed from the separation carousel and placed in the incubator carousel  57  middle ring by RV Handler  52   b . If required, the incubator carousel will also rotate the RV to accommodate any the addition of any other reagents. Incubator carousel  57  holds and agitates the RV until the incubation time is completed. Incubator carousel  57  then rotates the RV to a RV pickup position where the RV is removed by RV Handler  52   a  and delivered to detector robot  74 . 
     5.3.8 Wash Station Robot 
     Referring to  FIGS. 40-41 , according to one embodiment, a wash robot  62  includes a wash probe head and column assembly  610  a clean station, and a wash dispense probe  620 . Wash robot  600  aspirates waste fluids from reaction vessels while the separation carousel  55  holds the beads, by magnetic force, within the reaction vessels. The wash robot provides a uniform aspiration of liquid when aspirating from between one to four reaction vessels. The wash robot cleans all wash aspiration probes after use. Angled tip probes  612  are preferred to minimize probe blockage, however, blockage detection sensors are used to detect blockage of any wash aspiration probe. The wash system also provides the wash buffer for washing and re-suspending the beads. 
     Wash probe head and column assembly  610  move the wash probes vertically to the following positions: an RV aspirate position, a probe cleaning position and a ready position. Wash probe head  614 , to which one or more probes  612  are installed (e.g., two, four or more probes  612 ), is mounted on the top of the column  616 . Column  616  is driven vertically using a stepper motor  618  and belt drive. 
     Wash robot  62  includes sensors home position and steploss. For example, a wash probe vertical home optical sensor  622  (see  FIG. 41 ) determines the vertical home position of the wash probe head and column. This sensor is located on top of the wash robot housing. A wash probe rotational steploss optical sensor, optionally determines if steploss during the vertical movement of the wash probes  612  has occurred. An encoder wheel can be is mounted on the stepper motor  618 . Horizontal wash motor  630  and wash well are also optionally used. Motors  618 ,  630  and sensors, with as sensor  622  and  632  preferably communicate with system  10  through circuit board  634  and backplane  200 . 
     The clean station  62  is mounted on a tilting axis, which moves between a cleaning position and a retracted position. In the cleaning position, the clean station is rotated into the path of probes  612 . In the retracted position, the clean station is rotated out of the probe path. 
     A clean station home optical sensor optionally determines the tilt home position of the clean station. In one embodiment, a clean station home optical sensor is located on the rear of the wash probe housing and is tripped by a flag rotating on the stepper motor. 
     A wash probe blockage sensor optionally determines if a wash probe  612  is blocked. Such a wash probe blockage sensor is preferably a conductive type sensor with one end mounted in the clean station and the other on the wash probes  612 . If liquid remains in the clean station after cleaning, then the wash probes  612  did not perform the clean aspiration properly. 
     Wash dispense probe  620  is mounted on the right side of wash robot  600 . The Wash dispense probe  620  dispenses a measured amount of wash fluid into the RVs located on the separation carousel. A FMI micropump, located in the fluidics subsystem as described below, provides the wash fluid through a fluid line  636 . Wash dispense probe  620  is mounted on a retractable lever arm  624 , which allows the probe to be rotated out of the way for service intervention. 
     During typical operation of the wash robot  600  RV handler  52   b  removes an RV from incubator carousel  57  and places it on the separation carousel  55 . RV contains a mixture of sample, reagent and conjugate depending on how far the assay has progressed. Separation carousel  55  moves the RV under one of the four wash probes  612  (after a predetermined separation time to allow the magnets to collect the beads against the RV wall). Wash robot (in the ready state with its clean station retracted) then lowers the wash probes into the RV to remove the liquid. Liquid is aspirated from the RV through the wash probe, e.g., by a nominal 15 kPA vacuum. After aspirating fluid from the RV, wash robot  600  then raises the wash probes and clean station tilts forward under the wash probes. The Wash robot lowers the wash probes into the clean station and DI water fills the clean station. The liquid is aspirated from the clean station by a nominal 30 kPA vacuum. Wash robot then raises the wash probes and the clean station retracts. Next, the separation carousel moves the RV under the wash dispense probe, where wash dispense probe dispenses a measured amount of wash buffer into the RV. The amount of wash buffer depends on the type of assay being performed and the progress of the RV in the assay. 
     After a predetermined separation time to allow the magnets to collect the beads against the RV wall, the separation carousel then moves the RV under one of the four wash aspirate probes. The RV is again presented to the wash probes and the wash probe liquid aspiration is repeated. Depending on the type of chemistry being performed the washing of the beads can occur a number of times. 
     After the last wash, the RV is presented to the wash dispense probe and a resuspend volume of liquid is dispensed into the RV. Separation Carousel  55  moves the RV to the RV Handler  52   b  pickup position. RV Handler  53   b  then removes the RV from the separation carousel  55  and places it on the incubator carousel  57 . 
     5.3.9 Detector Transfer Robot Assembly 
       FIG. 42  shows a detector transfer robot  74 , or detector robot  74 , according to an embodiment of the present invention. Detector robot  74  generally includes a reaction vessel rotational arm and drive  650 , a waste disposal lever  652 , a clean station and drive  654 , and a detector module probe mount  656 . Detector robot  74  presents reaction vessels to a detector module probe (also termed “detector probe”, not shown) on mount  656  and disposes of the reaction vessels after sample aspiration. Detector robot  74  also cleans the detector probe between each use and provides a stable mounting platform for mounting the detector probe. 
     RV rotation arm and drive  650  moves an RV from the “putdown” position (e.g., by RV Handler  52   a  on incubator carousel  57 ) and presents it to the detector module probe for aspiration. A drive motor  658  attached to a lead screw  660  rotates and moves the arm vertically. The vertical movement is accomplished by rotating the arm until it hits a hard stop (in this case, the vertical structure, or vertical stainless steel rod  662 ), of detector robot  74 , then the lead screw  660  continues to turn, driving arm  664  vertically (either up or down). 
     Referring to  FIG. 43 , the following sensors monitor the position and movement of the RV rotational arm and drive  650 . A detector robot rotational home optical sensor  666  located on detector robot  74  housing is designed to determine the rotational and vertical home position of the detector robot  74 . A detector robot rotation step optical sensor  668  determines the rotational position of detector robot  74 . This sensor is located on the rotational gearing above motor  658 . Vertical positioning of the arm  664  is controlled by parameters set within the software. Vertical alignment is performed during instrument installation. After the initial alignment, modification of the alignment is only required when the distance between the detector module probe tip and the RV bottom exceeds 1.0 mm. An optimum distance is between 0.5-1 mm. 
     Referring again to  FIG. 42 , downward arm  664  motion at the pickup position triggers the action of the waste disposal lever  652 . When the arm moves down waste disposal lever pushes the RV out of the rotational arm  664  and into the waste chute  670 . Waste disposal lever  562  includes a prong and lever. The prong is used to push the RV up and out of the rotational arm  664  and the lever pushes the RV over into the waste chute  670 . 
     Clean station and drive  654  raises and lowers the clean station  672  to the detector module probe. Clean station and drive  654  also uses a drive motor  674  and lead screw  676  to vertically move clean station  672 . All the fluidics connections to the clean station are located on the bottom of the clean station. This allows the clean station to move freely up and down without tangling the fluidics tubing. Clean station  672  has multiple fluid lines, e.g., one input fluid line (for cleaning the outside of the probe) and two output fluid lines (one for draining the clean station and one as an overflow). 
     Referring back to  FIG. 43 , the following sensors monitor the status, position and movement of the clean station and drive  654 . Clean station home optical sensor  678 , located on detector robot  74  housing, determines the vertical home position of clean station  672 . Clean station vertical optical sensor  680 , located on the rotational gearing associated with motor  674  used to move clean station  672 , determines the vertical position of the clean station. Additionally, a clean station overflow sensor is a conductive sensor mounted on or within clean station  672  to monitor clean station for any blockage that would cause clean station  672  to overfill. 
     The detector module probe mount  656  secures the detector probe to the top of detector robot  74 . Detector Module probe is placed through the top of the mount  656  and secured using the threaded nut. The mounting position is adjustable by a slot and screw combination. The probe has holes, for example five holes of approximately 0.005 inch, or about 0.0127 mm, running through it and contains an internal screen. 
     During typical operation of detector robot  74 , rotational arm  664  moves to an RV acceptance position and RV Handler  52   a  places a RV in the RV holder  665  of rotational arm  664 . Rotational arm  664  rotates clockwise to below the detector module probe and raises the RV to the aspiration position for the Detector Module probe in probe mount  656  as shown in  FIG. 42 . Detector module probe aspirates the sample from the RV. After aspiration, rotational arm  664  lowers and rotates back to the pickup position. Rotational arm  664  then lowers causing the waste disposal prong to push the RV out of the rotational arm. Lowering the rotational arm activates spring loaded waste disposal lever  452  and the lever moves forward and pushes the RV into the waste chute  670 . Next, clean station  672  rises to clean the detector module probe and rotational arm  664  returns to the RV acceptance position. Clean station  672  lowers after cleaning the probe. 
     While detector transfer robot assembly  74  is described above as being an assembly within sample processing module  30 , robot assembly  74  may be part of or incorporated within detector module  20 . 
     5.3.10 RV Waste Assembly 
       FIGS. 44A and 44B  show a reaction vessel waste assembly  700  according to an embodiment of the present invention. Reaction vessel waste assembly  700  generally includes a reaction waste chute  670  (as described with respect to  FIG. 42 ), a reaction vessel buffer area  702 , a reaction vessel waste bin, and a reaction vessel waste level tracker. Reaction vessel waste system  700  preferably has quantity to accept waste from up to eight continuous hours of operation. A user of the device can remove and empty the waste bin  706  without interrupting the operation of the device. Reaction vessel waste bin  704 , e.g., located in solid waste compartment  64  of device  10  (see  FIG. 2 ) is easily accessible and fitted with biohazard bags for the collection of waste. The components of the reaction vessel waste system are accessible for easy cleaning. Furthermore, there is a monitoring system that monitors the waste system and determines the presence of a biohazard waste bag and monitors the level of waste, alerting the user when the waste requires emptying. 
     RV waste chute  670  is designed to catch the RVs dumped by the detector robot  74  as described above. A wide, sloping design (e.g., 30 degrees or more on all surfaces) ensures all RVs and liquid (contained within the RVs) are directed into the RV waste bin  704 . RV and liquid are not allowed to block or pool in chute  670 . Since the RV waste chute  670  will be interacting with waste (both RVs and their liquid), periodic cleaning of the chute is recommended. Chute is easily removed and cleaned by detaching it from its interface  708  with RV buffer area  702 . In this embodiment, lower end of chute  760  fits within an opening  710  on upper end of RV buffer  702 . 
     RV buffer  702  is designed to catch and hold RVs and their liquid waste whenever the RV waste bin  704  is extended or pulled out of the instrument chassis for waste removal. RV buffer  702  includes a main body  703  that interfaces with RV waste chute  670 , and a trap door  712 . Trap door  712  is located towards the bottom end of RV waste chute  760  and is hingeably attached at two connection points  714  to body  703  such that door  712  can move from a closed (i.e., blocking the passage of RVs and fluid to waste bin  704 ) to an open position as shown. One skilled in the art will recognize that other door or door attachment mechanisms may be used without departing from the scope of this invention. 
     In this embodiment, RV buffer  702  has the capacity to store approximately 1 hour worth of RV and liquid waste (e.g., approximately 100 RVs and approximately 2 ml of fluid). RV waste bin  704  holds trap door  712  in the open position as shown under normal operation. However, when RV waste bin  704  is extended (opened) for waste removal, trap door  714  moves to the closed position blocking passage of disposed RVs. RV buffer  702  preferably does not use any motors to move into position, rather door  712  moves between open and closed positions by either gravity or contact with waste bin  704 . Optionally, a buffer door latch or stop  716  limits forward travel of door  712  when in closed position. In other embodiments, buffer  702  employs spring mechanisms or the like to control door position. 
     RV buffer  702  preferably includes an optical sensor located in the waste chute or RV buffer area  702  to determine if trap door  712  is in an open or closed state, and to communicate the state to the user through the host PC  40  or some other indicator such as a visual (e.g., LED indicator) or audio indicator. 
     RV waste bin  704  is a pullout drawer, incorporating a handle  706  and slides  718 , capable of extending beyond the instrument footprint and is preferably is configured to accept standard biohazard bags, e.g., bags measuring approximately 14″×19″. A biohazard bag is secured within the RV waste bin  704 , for example by spring clips, to prevent the bag from tearing when the bin is opened or closed. A bag detection sensor monitors the presence of the bag. In one embodiment, bag detection sensors are a conductive spring loaded contact switch system that is opened by the presence of any plastic biohazard bag. Removal of the bag trips the conductive sensor, causing software in host PC to determine no bag is present. In such embodiment, bag detection sensors are two-wire connections to a moving cable attached to the RV waste drawer. 
     Computer software, e.g., in host  40 , also monitors RV waste bin  704  level by incrementing the number of RVs in the waste each time a RV is transferred to waste  700  by detector robot  74 . The level is reset to zero every time a bag change is detected. To provide accurate tracking of waste level, the bag detection sensors are activated as a background task during power up and continue until the instrument is powered down. The sensors are required to remain active when RV waste bin  704  is extended out on the drawer slides  718 , as this is the time when the user will remove the waste bag. The sensor cable, to allow the drawer, is coiled to prevent tangling when the drawer is open or closed. 
     5.3.11 Cleaning Station Design 
     Three types of clean stations are used. All cleaning stations are designed to effectively clean the probe (inside and out) and minimize the consumables  12  used. 
     The Specimen and Reagent Probe Clean Stations are two-stage type clean stations. First, all contaminated waste is disposed of directly down the waste tubing cleans the probe. Then, the probe moves over and down into a well where liquid from the probe cleans interior and exterior of the probe. 
     The Detector transfer probe clean station is similar to the Specimen Probe and Reagent Probe Clean station except the Clean Station is a single stage type clean. The probe interior and exterior is cleaned by wash liquid supplied by the probe, however the probe is not moved from a dirty waste disposal position to a clean probe position. The detector probe clean station is aligned physically in the x-y axis using slots in the clean station. The probe insertion depth is a software controlled variable. 
     The Wash Probe Clean Stations clean the probes by filling the clean station with wash liquid, then using the probes to drain the stations. In these stations, only a wash liquid supply is required. The liquid is drained only via the probes. The initial wash liquid supply cleans the outside of the probe and the draining via the probes cleans the interior. The probes are aligned physically in the horizontal axis (combination of x-y axes) using slots in the clean stations for positioning. The rotational alignment and probe insertion depth are software-controlled variables. 
     5.3.12 System Fluidics 
     5.3.12.1 Overview of System Fluidics 
       FIGS. 45-48  show a fluidics system  800  according to an embodiment of the present invention.  FIG. 45  shows a number of fluid and waste storage bottles, including buffer supply  802 , sheath supply  804 , DI water  806 , and waste  808 . Fluidics system  800  generally supplies buffers, including sheath, wash, and deionized water for use in detection, cleaning, and sample movement. For example, the system provides for the addition of liquids and disposal of waste without interruption of operation. Furthermore, the system also accurately aspirates and dispenses samples and reagents of various quantities. Additionally, the system accurately dispenses and aspirates wash buffer from reaction vessels, cleans the outside of all probes, and cleans the inside of all reagent and specimen probes.  FIGS. 45 and 46A  and  46 B are a block diagram and a detailed schematic diagram, respectively showing fluidics system  800  and the various related components and sensors described herein, many of which preferably, although not necessarily receive power from and communicate through fluidics circuit board  810 . 
     Internal bulk reagent and waste reservoirs as shown if  FIG. 45  contain enough capacity on board the device to allow all specimens currently in a process to be completed, should external supplies be exhausted. 
     Fluidics control system provides a wash buffer, sheath fluid for the detector and deionized water for cleaning probes. The fluidics control system incorporates at least three precision syringe pumps for specimen and reagent aspiration and dispense, and an FMI positive displacement dispensing pump for bead washing. 
     In one embodiment, the fluidics system includes a number of sub-subsystems, each of which are discussed in more detail below. 
     5.3.12.2 Details of Subsystems of System Fluidics 
     DI Water Subsystem #1 
     The DI Water Subsystem stores and delivers DI water to the other sub-systems. DI water is used to clean various probes, flush valves and components and perform periodic maintenance. Additionally, as an added option DI Water Subsystem can be directly plumbed into the instrument. 
     The DI Water Subsystem includes a Bulk DI Water Supply (e.g., 5 Liter Capacity), a customer accessible container with liquid level monitoring. The Bulk DI Water Supply has the capacity to supply the instrument with DI for an eight-hour continuous run. The liquid level sensing is used to notify the customer, via a software interface, when additional DI is required. This container is not pressurized or under a vacuum. 
     A DI Water Intake Pump pumps DI from the Bulk DI Water Supply to the Internal DI Water Supply. The pump is activated when the DI level in the Internal DI Water Supply falls below a specific level. A self-priming diaphragm pump is used in this capacity. 
     A DI Water Intake Check Valve prevents DI water from traveling from the Internal DI Water Supply to the Bulk DI Water Supply. The check valve (1.5 psi cracking pressure) is required because the Internal DI Water Supply bottle is pressurized. 
     An internal DI Water Supply such as a 1 Liter Capacity pressurized internal DI reservoir with liquid level monitoring. The low pressure provides the motive force to drive the DI water to the various pumps and clean station. The Internal DI Water Supply capacity is maintained to provide for the completion of all in-process assays should the Bulk DI Water Supply be exhausted or removed. A current minimum is 550 ml. An example of a DI water supply  850  is shown in  FIG. 48B . 
     DI Selector Valve—Provides either DI water or Wash Buffer to the Fluid Supply Manifold depending on the valve position. 
     Fluid Supply Manifold—Provides either DI water or Wash Buffer to the various pumps and clean stations contained within the other sub-systems. The DI Selector Valve controls the supply of fluids (either DI or Wash Buffer) to the Fluid Supply Manifold. 
     Tubing and Fittings—Various small diameter tubing and fittings used to connect the components. 
     The DI Water Supply preferably has a number of sensors, for example six sensors. A thermistor type sensor is used in all DI Water sensing situations due to the non-conductive nature of DI Water. Thermistors are semiconductors that will change resistance with a change in temperature. As the DI Water covers or uncovers the thermistor, the resistance of the thermistor changes. In both the Bulk and Internal DI Water, three thermistors are used to correctly sense DI Water liquid levels. 
     Bulk DI Water Supply Cap Sensor—Monitors the ambient temperature and provides a reference point for the software to identify changes in liquid levels at the low and high liquid level sensors. 
     Bulk DI Water Supply Low Liquid Level Sensor—Monitors the low liquid level within the Bulk DI Water Supply. When tripped, this sensor causes the software interface to notify the customer that additional Bulk DI Water is required. 
     Bulk DI Water Supply High Liquid Level Sensor—Monitors the high liquid level within the Bulk DI Water Supply. When tripped, this sensor causes the software interface to notify the customer that Bulk DI Water is full. 
     Internal DI Water Supply Cap  826  Sensor—Monitors the ambient temperature and provides a reference point for the software to identify changes in liquid levels at the low and high liquid level sensors. 
     Internal DI Water Reservoir Low Liquid Level Sensor  822 —Monitors the low liquid level within the Internal DI Water Reservoir. When tripped, this sensor causes the Internal DI Reservoir to be filled from the Bulk DI Water Supply via the DI Intake pump (provided bulk DI water is present). 
     Internal DI Water Reservoir High Liquid Level Sensor  824 —Monitors the high liquid level within the Internal DI Water Reservoir. When tripped, this sensor stops the filling of the Internal DI Reservoir. 
     Wash Buffer Subsystem #2 
     The Wash Buffer Subsystem stores and delivers Wash Buffer to the other sub-systems. Wash Buffer is used as a hydraulic fluid, bead washing and re-suspension, probe cleaning fluid and specimen diluent. The Wash Buffer Subsystem includes the following components. 
     A Bulk Wash Buffer Supply—10 Liter Capacity—A customer accessible container with liquid level monitoring. The Bulk Wash Buffer Supply has the capacity to supply the instrument with Wash Buffer for an eight-hour continuous run. The liquid level sensing is used to notify the customer, via a software interface, when additional Wash Buffer is required. This container is not pressurized or under a vacuum. 
     A Wash Buffer Intake Pump—Pumps Wash from the Bulk Wash Buffer Supply to the Internal Wash Buffer Supply. The pump is activated when the Wash Buffer in the Internal Wash Buffer Supply falls below a specific level. A self-priming diaphragm pump is used in this capacity. 
     A Wash Buffer Intake Check Valve—Prevents Wash Buffer from traveling from the Internal Wash Buffer Supply to the Bulk Wash Buffer Supply. The check valve (1.5 psi cracking pressure) is required because the Internal Wash Buffer Supply bottle is pressurized. 
     An Internal Wash Buffer Supply—1 Liter Capacity—A pressurized internal Wash Buffer reservoir with liquid level monitoring. The pressure provides the motive force to drive the Wash Buffer to the various pumps and clean station. The Internal Wash Buffer Supply capacity is always maintained to provide for the completion of all in-process assays should the Bulk Wash Buffer Supply be exhausted or removed. An example of a current minimum is 550 ml, as shown in the example internal wash buffer supply  830  of  FIG. 48A . 
     A DI Selector Valve—Provides either DI water or Wash Buffer to the Fluid Supply Manifold depending on the valve position. 
     A Fluid Supply Manifold—Provides either DI water or Wash Buffer to the various pumps and clean stations contained within the other sub-systems. The DI Selector Valve controls the supply of fluids (either DI or Wash Buffer) to the Fluid Supply Manifold. 
     Tubing and Fittings—Various small diameter tubing and fittings used to connect the components. 
     In a preferred embodiment, Wash Buffer Supply has four sensors  832 ,  834 ,  836 ,  838 , which are preferably conductive sensors. In one embodiment, the sensors are stainless steel probes with a voltage applied to them. Wash Buffer completes a circuit between the probe and a common probe to trip the sensor. The common probe is also a stainless steel probe.
         Bulk Wash Buffer Supply Low Liquid Level Sensor—Monitors the low liquid level within the Bulk Wash Buffer Supply. When tripped, this sensor causes the software interface to notify the customer that additional Wash Buffer is required.   Bulk Wash Buffer Supply High Liquid Level Sensor—Monitors the high liquid level within the Bulk Wash Buffer Supply.   Internal Wash Buffer Reservoir Low Liquid Level Sensor  834 —Monitors the low liquid level within the Internal Wash Buffer Reservoir. When tripped, this sensor causes the Internal Wash Buffer Reservoir to be filled from the Bulk Wash Buffer Supply (provided Wash Buffer is present). The sensor is currently set to trip when the internal capacity falls below 550 ml.   Internal Wash Buffer Supply High Liquid Level Sensor  836 —Monitors the high liquid level within the Internal Wash Buffer Reservoir. When tripped, this sensor stops the filling of the Internal Wash Buffer Reservoir.
 
Sheath Subsystem #3
       

     The Sheath Subsystem stores and delivers sheath to the Detector Module. Sheath is supplied to the Detector Module in both a precision metered flow and a non-pressurized flow. 
     The Sheath Subsystem includes of the following components;
         Bulk Sheath Supply—5 Liter Capacity—A customer accessible container with liquid level monitoring. The Bulk Sheath Supply has the capacity to supply the instrument with Sheath for an eight-hour continuous run. The liquid level sensing is used to notify the customer, via a software interface, when additional Sheath is required. This container is not pressurized or under a vacuum.   Sheath Intake Pump—Pumps Sheath from the Bulk Sheath Supply to the Internal Sheath Supply. The pump is activated when the Sheath level in the Internal Sheath Supply falls below a specific level. A self-priming diaphragm pump is used in this capacity.   Sheath Intake Check Valve—Prevents Sheath from traveling from the Internal Sheath Supply to the Bulk Sheath Supply. The check valve (1.5 psi cracking pressure) is required because the Internal Sheath Supply is pressurized.   Internal Sheath Supply—1 Liter Capacity—An internal Sheath reservoir with liquid level monitoring. Either the Sheath Fluid Gear Pump or the Detector Module Syringe Pump draws the Sheath from the Internal Sheath Supply. The Internal Sheath Supply capacity is always maintained to provide for the completion of all in-process assays should the Bulk Sheath Supply be exhausted or removed. The current minimum is 550 ml.   Detector Module Sheath Fluid Gear Pump—Provides Sheath from the Internal Sheath Supply at a precise flow rate (90 uL/sec+5%) to the Detector Module Cuvette. The importance of the flow rate to the success of this technology requires the use of an extremely high quality pump.   Syringe Pump Filter (1 μm)—Filters the Sheath prior to use by the Detector Module Syringe Pump.   Tubing and Fittings—Various small diameter tubing and fittings used to connect the components.       

     The Sheath Supply has five sensors. Conductive sensors are used in Sheath. The sensors are simple stainless steel probes with a voltage applied to them. Sheath completes a circuit between the probe and a common probe to trip the sensor. The common probe is also a stainless steel probe.
         Bulk Sheath Supply Low Liquid Level Sensor—Monitors the low liquid level within the Bulk Sheath Supply. When tripped, this sensor causes the software interface to notify the customer that additional Sheath is required.   Bulk Sheath Supply High Liquid Level Sensor—Monitors the high liquid level within the Bulk Sheath Supply. o Internal Sheath Reservoir Low Liquid Level Sensor—Monitors the low liquid level within the Internal Sheath Reservoir. When tripped, this sensor causes the Internal Sheath Reservoir to be filled from the Bulk Sheath Supply (provided Sheath is present).   Internal Sheath Supply Mid Liquid Level Sensor—Monitors the mid liquid level within the Internal Sheath Reservoir. This sensor ensures enough Sheath fluid is present within the reservoir to complete processing of all aspirated samples in the instrument. When tripped, this sensor stops the filling of the Internal Wash Buffer Reservoir.   Internal Sheath Supply High Liquid Level Sensor—Monitors the high liquid level within the Internal Sheath Reservoir. When tripped, this sensor stops the filling of the Internal Sheath Reservoir.
 
Wash, Separate and Re-Suspend Subsystem #4
       

     The Wash, Separate and Re-Suspend System, aspirates liquid from RVs, disposes of aspirated waste, cleans Wash Probes, dispenses Wash Buffer to RVs. The Wash, Separate &amp; Re-Suspend Subsystem consists of the following components;
         Wash Dispense Pump (FMI type)—Pumps accurately metered volumes of Wash Buffer to the Wash Dispense Probe. The amount of liquid pumped is dependent on the washing and re-suspension requirements for each individual assay.   Wash Dispense Probe—Dispenses the Wash Buffer provided by the Wash Dispense Pump into the RV.   Wash Probes—Aspirates liquid from RVs in the Separation Carousel. The Wash Probe Robot lowers the four Wash Probes into the RVs. The Wash Probes are positioned (aligned) to provide a consistent liquid aspiration in any RV position. The depth of probe insertion is optimized to remove liquid and retain bead (in the bead patch).   Wash &amp; Separate Waste Container—Collects all liquid waste aspirated through the Wash Probes. This container serves as a temporary storage for liquid waste being moved from the Wash Probes to the Internal Waste Containers.   Wash Waste Valve—Allows liquid waste to be drawn from temporary storage (Wash &amp; Separate Waste Container) to Waste Management System.   Wash &amp; Separate Clean Valve—Allows DI Water to flow into the Wash Probe Clean Station.   Wash Probe Clean Station—Presents four individual clean stations (as a group) to the Wash Probes. The clean station is fitted with liquid level sensing to identify blockages in the Wash Probes. If liquid remains in one of the clean stations after aspiration, then the probe must be blocked.   Tubing and Fittings—Various small diameter tubing and fittings used to connect the components. The Wash, Separate &amp; Re-Suspend System has two sensors. Both of these sensors are conductive sensors that use liquid to trip the sensor.   Wash Probe Clean Station Liquid Level Sensor—Monitors the liquid within the Wash Probe clean station. Since each probe has its own clean station (well), the sensor monitor the liquid within the well. If liquid remains in any of the wells after cleaning, the sensor is tripped. This presence of liquid indicates the blockage of one or more of the Wash Probe. The customer is notified of this and directed to take corrective action.   Wash Separate Waste Reservoir Sensor—Monitors the liquid waste level within the Wash Separate Waste Container. The sensor is mounted in the top of the container and is tripped when liquid fills the container. Under normal operation, liquid does not remain in the container.
 
Reagent Transfer Subsystem #5
       

     The Reagent Transfer Subsystem aspirates and dispenses reagents as well as cleaning the Reagent Probe. The Reagent Robot physically transfers reagents from the Reagent Carousel to RVs on the Incubator Carousel. The Reagent Transfer Subsystem includes the following components:
         Reagent Syringe Pump—A highly accurate 2.5 ml cavro syringe pump used to aspirate and dispense reagent and push DI Water through the Reagent Probe for cleaning   Reagent Probe—Aspirates and dispenses reagents.   Reagent Clean Station—A fixed mounted clean station for the Reagent Probe. DI Water is pumped into the clean station when the Reagent Clean Valve is opened.   Reagent Clean Valve—Allows DI Water to flow into Reagent Clean Station. o Reagent Waste Valve—Allows liquid waste to flow from the clean station to the Waste Management System.   Tubing and Fittings—Various small diameter tubing and fittings used to connect the components. The Reagent Transfer System has two sensors.   Reagent Probe Blockage Detection Unit—Monitors the vacuum and pressure used to aspirate and dispense reagent. If the Reagent Probe becomes blocked the vacuum or pressure will increase, tripping the sensor. The customer is notified of this and directed to take corrective action, such as cleaning or replacing the probe.   Reagent Probe Liquid Level Sensor—Detects when the Reagent Probe comes in contact with reagents. The change in capacitance is determines liquid contact. The software ensures the probe is inserted far enough for reagent aspiration, and calculates of reagent supplies remaining within the reagent pack uses this liquid level sensing.
 
Specimen Transfer Subsystem #6
       

     The Specimen Transfer Subsystem aspirates, moves and dispenses specimen samples into RVs on the Incubator Carousel. Additionally, it cleans the Specimen Probe and disposes of the waste. The Specimen Transfer includes the following components.
         Specimen Syringe Pumps—Two highly accurate cavro syringe type pumps used to aspirate sample from sample tubes and dispense into RVs. The 2.5 ml pump is used exclusively for cleaning of the probe while the 250 μl pump is used for sample aspiration and dispense.   Specimen Clean Syringe Pump o Blockage Detection Fitting—A sensor designed to determine if the Specimen Probe is blocked. It is located on the tubing between the Specimen Probe and Specimen Aspirate Syringe Pump.   Specimen Probe—Aspirates and dispenses sample. o Specimen Probe Clean Station—A fixed mounted clean station for the Specimen Probe. DI Water is pumped into the clean station when the Specimen Probe Clean Valve is opened.   Specimen Probe Clean Valve—Allows DI Water to flow into the Specimen Probe Clean Station.   Specimen Waste Valve—Allows liquid waste to flow from the clean station to the Waste Management System.   Tubing and Fittings—Various small diameter tubing and fittings used to connect the components.       

     The Specimen Transfer System preferably has two sensors, including a Specimen Probe Blockage Detection Unit that monitors the vacuum and pressure used to aspirate and dispense specimen. If the Specimen Probe becomes blocked the vacuum or pressure will increase, tripping the sensor. The customer is notified of this and directed to take corrective action, such as cleaning or replacing the probe. A Specimen Probe Liquid Level Sensor can be used to detect when the Specimen Probe comes in contact with specimen. The change in capacitance is determines liquid contact. The software ensures the probe is inserted far enough for reagent aspiration. 
     Detector Module Fluid Transfer Subsystem #7 
     The Detector Module Fluid Transfer Subsystem removes Detector Module waste and cleans the probe. The Detector Module Fluid Transfer Subsystem includes the following components:
         Detector Module Clean Station—A vertical moving clean station for cleaning the Detector Module Probe.   Detector Module Clean Valve—Allows DI Water to flow into the Detector Module Clean Station. DI Water is pumped into the clean station when the Detector Module Clean Valve is opened.   Detector Module Probe Waste Valve—Allows liquid waste to flow from the clean station to the Waste Management System.   Detector Module Probe—A fixed mounted probe through which processed samples are drawn into the Detector Module.   Tubing and Fittings—Various small diameter tubing and fittings used to connect the components.   The Detector Module Fluid Transfer System contains a single sensor relating to the Fluidics.   Detector Clean Station Overflow Sensor—A conductive sensor, located in the top of the Clean Station, that monitors the clean station overfill for liquid. This sensor is designed to monitor the clean station or its tubing and trigger an error when they become blocked.
 
Waste Management Subsystem #8
       

     The Waste Management System removes and stores waste from the other sub-systems. The customer disposes of stored waste. Additionally, as an option the Waste Management System can be directly plumbed into an existing waste disposal system. The Waste Management System includes of the following components;
         Two General Purpose Waste Container—A general temporary waste collection containers (each 1 liter capacity). Typically, liquid waste from the clean stations, drains and clean station overflow is collected here, and then transferred to the Internal Waste Containers.   General Purpose Waste Valve—Allows liquid waste to flow from the General Purpose Waste Container to the General Purpose Manifold.   General Purpose Manifold—Acts as a five-function manifold to processes a wide variety of liquids (waste, Wash Buffer, and DI Water) to various components of the Fluidics System. Each function is independent of all other functions (within the manifold) and are described in the following:       

     Function 1; Collects waste from the General Purpose Waste Container and Wash &amp; Separate Waste Container and delivers it to the Waste Delivery Manifold. 
     Function 2; Processes Wash Buffer from the Internal Wash Buffer Reservoir to the Fluid Supply Manifold. The DI Selector Valve controls the flow of Wash Buffer. 
     Function 3; Provides a path for regulated low vacuum to be monitored on the Fluidics Control Board and supply vacuum to the Wash &amp; Separate Waste Container. 
     Function 4; Processes DI Water from the Internal DI Water Reservoir to the Fluid Supply Manifold (controlled by the DI Selector Valve) and Wash Probe Clean Station (controlled by the Wash &amp; Separate Clean Valve). 
     Function 5; Processes liquid waste from Detector Module Clean Station, Reagent Probe Clean Station, and Specimen Probe Clean Station to the Waste Delivery Manifold.
         Waste Delivery Manifold—Acts as a four-function manifold to process liquid waste and deliver vacuum and pressure to components requiring them. Each function is independent of the other functions (within the manifold) and are described below.       

     Function 1; Collects liquid waste from General Purpose Manifold and delivers is to the Internal Waste Containers. 
     Function 2; Provides a path for unregulated pressure and vacuum to enter the Waste Management System. The Pressure/Vacuum Selector Valve determines if pressure or vacuum is supplied. Upon exit of the manifold the Waste Changeover Valve determines the destination of the pressure or vacuum. 
     Function 3; Provides a path for a regulated high vacuum to be monitored on the Fluidics Control Board and supply vacuum to the Internal Waste Reservoirs. 
     Function 4; Provides a path for a regulated pressure to be monitored on the Fluidics Control Board, pressurize the Internal Wash Buffer and DI Water Reservoirs and pressurize the Internal Waste Container.
         Waste Changeover Valve—Selects which output (waste and vacuum or pressure) from the Waste Delivery Manifold is delivered to the Bottle Selector Waste Manifold. Selecting waste and vacuum output, draws waste to the Internal Waste Containers (from the various sub-assemblies). While selecting pressure output, pushes waste from the Internal Waste Container to the Bulk Waste Container.   Bottle Selector Waste Manifold—Delivers the selected output (waste and vacuum or pressure) from the Waste Changeover Valve to the Internal Waste Containers. The Waste Changeover Valve determines the output delivery and the manifold simply delivers it to the desired location.   Internal Waste Containers (Qty—2)—Provide liquid waste storage with a holding capacity of eight hours of instrument operation. During normal operation, only one container is filled at a time. Each container has three liquid level sensors. A low level sensor indicates the container is present (the container will never empty below this level, so if the sensor registers liquid, a container must be present). A mid level sensor to ensure that all the samples in-process on the instrument can be completed. This is used to ensure all in-process samples can be completed without the removal of any waste. A high level sensor to determine when a container is full.   Purge Selector Valve—Determines which Internal Waste Container will be purged to the Bulk Waste Containers.   Purge On/Off Valve—Allows the Internal Waste Containers to be purged to the Bulk Waste Containers.   Bulk Waste Selector Valve—Determines which Bulk Waste Container waste is purged to from the Internal Waste Containers.   Bulk Waste Containers—10 liter capacity (Qty 2)—Provides bulk liquid waste storage. The customer is required to remove and empty the waste in these containers. Each container has a high liquid level sensor to determine when the container is full.   Tubing and Fittings—Various small diameter tubing and fittings used to connect the components. The Waste Management System has ten sensors. All sensors within the Waste Management System are conductive type.   GP Waste Container High Liquid Level Sensor—Monitors the high liquid level within the GP Waste Container. When tripped this sensor, initiates the removal of waste from the GP Waste Container.   GP Waste Container Low Liquid Level Sensor—Monitors the low liquid level within the GP Waste Container. When tripped, this sensor stops the removal of waste from the GP Waste Container.   Internal Waste Container  1  High Liquid Level Sensor—Monitors the high liquid level waste within the Internal Waste Container  1 . When tripped, this sensor prevents additional waste from being added to the container (assumes the container is full).   Internal Waste Container  1  Mid Liquid Level Sensor—Monitors the mid liquid level waste within the Internal Waste Container  1 . This sensor ensures the waste container contains adequate capacity to process all waste from samples currently being processed.   Internal Waste Container  1  Low Liquid Level Sensor—Monitors the low liquid level waste within the Internal Waste Container  1 . Since a certain amount of liquid should always be present in the container, the tripping of this sensor indicates the bottle has been removed. When tripped, this sensor prevents additional waste from being added to the container.   Internal Waste Container  2  High Liquid Level Sensor—Monitors the high liquid level waste within the Internal Waste Container  2 . When tripped, this sensor prevents additional waste from being added to the container (assumes the container is full).   Internal Waste Container  2  Mid Liquid Level Sensor—Monitors the mid liquid level waste within the Internal Waste Container  2 . This sensor ensures the waste container contains adequate capacity to process all waste from samples currently being processed. o Internal Waste Container  2  Low Liquid Level Sensor—Monitors the low liquid level waste within the Internal Waste Container  2 . Since a certain amount of liquid should always be present in the container, the tripping of this sensor indicates the bottle has been removed. When tripped, this sensor prevents additional waste from being added to the container.   Bulk Waste Container  1  High Liquid Level Sensor—Monitor the high liquid level waste within the Bulk Waste Container  1 . When tripped, this sensor prevents additional waste from being added to the container (assumes container is full).   Bulk Waste Container  2  High Liquid Level Sensor—Monitor the high liquid level waste within the Bulk Waste Container  2 . When tripped, this sensor prevents additional waste from being added to the container (assumes container is full).
 
Pressure Subsystem #9
       

     The Pressure Subsystem creates, stores and delivers pressure to the other sub-systems. Pressure is used to transfer fluids by other sub-systems. The Pressure Subsystem includes the following components.
         Pressure Pump—Supplies pressure to the Pressure Accumulator. The pressure Accumulator holds pressure until needed by the instrument. The Accumulator Pressure Sensor on the Fluidics Control Board monitors the pressure.   Pressure Regulator—Regulates the pressure supplied to the Waste Delivery Manifold.   Regulated Pressure Sensor—Monitors the regulated pressure on the Waste Delivery Manifold.   Accumulator Pressure Sensor—Monitors the pressure in the Pressure Accumulator.   Pressure/Vacuum Selector Valve—Determines if pressure or vacuum are delivered to the Waste Delivery Manifold   Tubing and Fittings—Various small diameter tubing and fittings used to connect the components. The Pressure System has two sensors.   Accumulator Pressure Sensor—Monitors the pressure within the Pressure Accumulator. The pressure is measured at the accumulator. The sensor is located on the Fluidics Board.   Regulated Pressure Sensor—Monitors the regulated pressure used by the DI Water and Wash Buffer Supplies. The regulated pressure is measured at the Waste Delivery Manifold and only during instrument warm up to ensure the regulator is functioning properly. The sensor is located on the Fluidics Board.
 
Vacuum Subsystem #10
       

     The Vacuum Subsystem creates, stores and delivers vacuum to the other sub-systems. Vacuum is used to transfer fluids by the other sub-systems. The Vacuum Subsystem includes of the following components;
         Vacuum Pump—Supplies vacuum to the Vacuum Accumulator   Vacuum Accumulator—Holds vacuum until needed by the instrument. A liquid level sensor monitors the Vacuum Accumulator to prevent liquid from being draw in.   High Vacuum Regulator—Regulates the high vacuum supplied to the Waste Delivery Manifold.   Regulated High Vacuum Sensor—Monitors the high vacuum at the Waste Delivery Manifold.   Regulated Low Vacuum Sensor—Monitors the low vacuum at the General Purpose Manifold.   Accumulator Vacuum Sensor—Monitors the vacuum levels within the Vacuum Accumulator.   Tubing and Fittings—Various small diameter tubing and fittings used to connect the components. The Vacuum System has four sensors.   Accumulator Vacuum Sensor—Monitors the vacuum within the Vacuum Accumulator. The vacuum is measured at the accumulator. The sensor is located on the Fluidics Board.   Accumulator Liquid Level Sensor—Monitors the amount of liquid within the Vacuum Accumulator. The addition of liquid to the Vacuum Accumulator is the indication of a problem.   Regulated Low Vacuum Sensor—Monitors the low regulated vacuum used by the Wash Buffer Supply and the Wash, Separate &amp; Re-Suspend System and only between washes during sample processing. The low regulated vacuum is measured at the General Purpose Manifold. The sensor is located on the Fluidics Board.   Regulated High Vacuum Sensor—Monitors the high-regulated vacuum used by the Waste Management System. The high-regulated vacuum is measured at the Waste Delivery Manifold and only during instrument warm up to ensure the regulator is functioning properly. The sensor is located on the Fluidics Board.
 
Fluidics PCB #11
       

     Although the Fluidics PCB is technically part of the Electronics section, it is important to discuss some of its function here to understand the operation of the Fluidics system. The Fluidics PCB provides a central location for all control and sensor connections in the Fluidics system. This design minimizes the length of wiring required and increases serviceability of the Fluidics system. The Fluidics PCB has the five pressure and vacuum (3 pressure, 2 vacuum) sensors located on it. They are connected to the various other components by tubing. The placement of the sensors on the Fluidics Board allows the sensor size to be minimized while maximizing reliability. 
     The Fluidics System performs a large number of tasks in both serial and parallel. To understand the Fluidics System, it is helpful that the workings of the pressure and vacuum are understood. The pressure side and vacuum side work in tandem to perform the various tasks required of the fluidics system by the instrument. The fluidics system is controlled by the electronics and computer system of the instrument. It should be noted that during any task performed by the fluidics system, the electronics and computer system must control both the pressure and vacuum sides. Failure to do so will result in the fluidics system being unable to successfully complete its assigned task. 
     5.3.12.3 Internal Reservoir Sensing 
     The five internal reservoirs within the instrument allow replacement of the external bulk bottles without interruption of instrument operation. The electrical connection and liquid level sensing probes are the same or similar on four of them (Wash Buffer, Sheath, and two Waste). 
     The four reservoirs optionally are configured as shown in  FIG. 48A  and using the following configuration of liquid level sensing probes 
     
       
         
           
               
             
               
                 TABLE 18 
               
             
            
               
                   
               
               
                 Examples of liquid level sensing probes. 
               
            
           
           
               
               
               
               
               
               
            
               
                 Reservoir 
                 Probe #1 
                 Probe #2 
                 Probe #3 
                 Probe #4 
                 Fluid Pick Up Line 
               
               
                   
               
               
                 Sheath 
                 0 V Reference (55 ml 
                 550 ml 
                 900 ml 
                 55 ml Probe 
                 Yes. At bottom of 
               
               
                   
                 Volume) 
                 Probe 
                 Probe 
                 (Blanking Probe) 
                 bottle (55 ml) 
               
               
                 Buffer 
                 0 V Reference (55 ml 
                 550 ml 
                 900 ml 
                 55 ml Probe 
                 Yes. At bottom of 
               
               
                   
                 Volume) 
                 Probe 
                 Probe 
                 (Blanking Probe) 
                 bottle (55 ml) 
               
               
                 Waste (2) 
                 0 V Reference (55 ml 
                 550 ml 
                 900 ml 
                 55 ml Probe 
                 Yes. At bottom of 
               
               
                   
                 Volume) 
                 Probe 
                 Probe 
                   
                 bottle (55 ml) 
               
               
                   
               
            
           
         
       
     
     The DI water reservoir liquid level sensing is configured as shown in  FIG. 48A . 
     5.4 Host Computer System 
     Referring back to  FIG. 1 , host computer system  40  of the MAD system  10  preferably includes a processor, a user in, keyboard, trackball for data entry, touch screen, VGA high resolution monitor, printer, and software. The computer system preferably has a dual microprocessor, one gigabyte of RAM memory, two 40 gigabyte hard drives, and a dual asynchronous serial interface. The computer system is responsible for carrying out all of the necessary operations from instrument control to results evaluation, data storage, quality control, mainframe bidirectional interfacing, and operator assistance. The computer system is connected to the analyzer through two USB ports, while the printer is operated through a parallel port. The computer system has a LAN and a modem line connector. 
     The MAD system hardware and software provide complete control of the flow cytometer and performs real-time classification of the microspheres and analysis of the microsphere-based reactions simultaneously. The hardware includes a personal computer interface card that provides communication between the computer and the flow cytometer. The interface card has an on-board, high-speed digital signal processor that is capable of performing &gt;30 million mathematical functions per second. The software is a WINDOWS2000/XP®-based 32-bit application that provides a “multiplexed mode” for automated multiplexed analysis, as well as a “data acquisition mode” for nonautomated gating and data acquisition. In addition, statistical analysis generated by the software is recorded to comma-separated-value (CSV) files that can be read by third-party spreadsheet programs. 
     The instrument control software is in excess of 100,000 lines of C++ code, running under the QNX multi-threaded real time operating system, and performs all instrument control, specimen process scheduling, and error handling operations. Furthermore, instrument code can be upgraded or changed from the host via the USB interface or over a network from a remote server. 
     Turning now to the software component of the MAD system, the host software includes instructions for operating and controlling the multiple robots incorporated in the device. Furthermore, the host software controls movement of samples, pipetting samples, pipetting reagents, flushing samples, analyzing samples, reporting data, and troubleshooting the device. 
     In one embodiment, the MAD system software is divided into the following blocks: 
     (A) RUN—execution and evaluation of testing; 
     (B) Quality Control—long term quality control; 
     (C) System Parameter—operational programming, e.g., test applications, mainframe interface configurations, and calculations mode; and 
     (D) System Functions—system tests and troubleshooting System operators spend the majority of their time in the RUN block. The RUN block is discussed below in some detail. 
     To begin a run the operator first enters the patient requisition information which includes the patient name/number and the test(s) or panel selections. Patient demographics may also be entered now or, for better time efficiency, after the run has begun. Several operator defined functions exist to allow for rapid requisition entries. After the sample requests are ordered, it is possible to segregate the samples or specific assays. 
     In addition to the flexible sample handling, options are also provided for the run&#39;s calibration curve and controls. For each run the operator may choose from: (1) a full calibration curve, (2) one or two point adjustment, or (3) no calibrator, using the stored curve. Calibrators are run in duplicate and samples are run singularly. As many as three controls may be run per assay panel. 
     Other important functions of the RUN block include loading status, run optimization, run status, documentation, data conclusion/archive, and system cleaning What follows is a brief overview of each of these modules. Loading status provides a printed summary of the requested run. This load list includes all bulk solutions, reagents, samples, cleaning solution, and RVs; it indicates their volumes required for the run, and provides the appropriate numbered position for each constituent on the reagent, sample, and incubator rotors. 
     One of the functions of the software is to calculate the appropriate pipetting sequences. This feature allows the assays of a specific run to be performed during the shortest possible time period and thus optimize the workload management. 
     The “Run” status allows the operator to determine at any time the system&#39;s progress in the run. It shows the individual procedural steps of pipetting, incubation, washing, and flow cytometric measurements for each assay in the run, including their start and end times. 
     5.5 Examples 
     5.5.1 General Method of Use of a MAD Instrument and System 
     In a preferred embodiment, a MAD instrument and system  10  allows for simultaneous detection of multiple analytes a single sample. Hence, the instrument makes possible a “multi-analyte detection system.” The system is designed to simultaneously detect the presence of multiple different (up to approximately 25) antibodies in a test sample (e.g., a blood sample). This system utilizes the following basic steps: 
     1) A test sample to be analyzed for the presence of one or more “analytes” of interest is contacted with a population of magnetic beads. A bar code is used to identify the test sample. In such a system, the analytes are particular antibodies that may be present in the test sample. Different beads within the population exhibit different particular combinations of fluorescent dyes and “analyte detectors.” In a current embodiment, the analyte detectors are particular antigens. Each analyte detector binds a particular analyte to be detected. Specifically, each magnetic bead is uniquely dyed with two distinct fluorescent dyes. Thus, in the current BioPlex 2200 system, each analyte detector antigen binds a particular analyte antibody. The dyes are preferably oil-soluble or hydrophobic and the dyes are incorporated into the bead rather than being attached to the bead&#39;s surface. Each dye can have any of ten (10) or more possible levels of fluorescent intensity, thus creating a family of up to one hundred (100) or more spectrally addressed (color coded) beads. Any particular magnetic bead is identified via a specific combination of fluorescent dyes (the combination is referred to collectively as a “classification dye”) the bead exhibits. Each magnetic bead exhibiting a particular classification dye also exhibits a particular analyte detector (antigen). Thus, by detecting a particular classification dye of a magnetic bead, one also identifies the specific analyte detector (antigen) the magnetic bead exhibits. Generally, the test sample and magnetic beads are incubated for approximately 15 minutes at 37° C. inside the instrument reaction vessel. 
     2) After incubation, the magnetic beads are washed (generally three times) to remove unbound test sample material. Specifically, when the reaction vessel is ready to be washed, a magnetic field is applied that draws the magnetic beads to the wall of the reaction vessel, where they are maintained during washing. After each washing, the magnetic field is removed and the beads are resuspended. One skilled in the art will appreciate that the beads and/or magnets may incorporate various types of materials that either produce or respond to magnetic fields such that the beads are attracted to the side of a reaction vessel during washing. 
     3) After washing, the only antibodies remaining in the reaction vessel are those that had bound to antigens present on the now washed magnetic beads. The washed magnetic beads, some or all of which may have bound analytes (antibodies of interest) present in the test sample, are then contacted with a labeled reporter molecule that is a fluorescently labeled secondary antibody designed to bind to any antibody (e.g., any human antibody or any particular class of human antibody) left remaining in the reaction vessel. Thus, those magnetic beads that bound an antibody from the test sample will, in this step, also bind a labeled reporter molecule. Generally, the beads and the labeled reporter molecule are incubated in the reaction vessel for approximately 15 minutes at 37° C. 
     4) The magnetic beads are then washed again to remove any unbound labeled reporter molecules, as described in 2), above. 
     5) At this point, those antibodies from the test sample that had bound to the magnetic beads have been bound by a labeled reporter molecule. The reaction vessel containing the magnetic beads is introduced to the detector module  20 . In this example, a suitable detector module includes flow cytometry mechanisms and at least two lasers. The two lasers are a red 635 nm classification laser and a green 532 nm reporter laser. The magnetic beads are then analyzed via flow cytometry involving a two laser system, in which one laser can detect and identify a classification dye and the second can detect the labeled reporter molecule. The identification of a particular classification dye passing through a particular flow cell indicates what analyte detector (antigen) the magnetic bead carries. If that bead is also determined to have bound a labeled reporter molecule, then the test sample contains the analyte (antibody) the particular magnetic bead is designed to detect. As all the magnetic beads are evaluated together via this two laser system, the presence of each of the multiple analytes (antibodies) is evaluated simultaneously. The results are read, collated and displayed and/or stored by a computer. 
     As pointed out above, the detector module in this example utilizes flow cytometry technology employing two lasers of different frequencies. One laser excites the fluorescent dye in the bead to identify the bead that just has passed through the flow cell by detecting the bead classification dye. The other laser excites the fluorescent dye bound to the labeled reporter molecule to indicate that an antibody from the test sample is bound to the magnetic particle. 
     In particular, the detector module in this example involves two solid-state lasers. First, a red diode classification laser excites fluorochromes embedded through the dyes of the bead. When the red diode classification laser illuminates a dyed bead, the bead&#39;s fluorescent signature identifies it as a particular member of one of the species of classification dyes (a qualitative analysis). Software correlates the bead species to the particular analyte detector (antigen) present on the magnetic bead. Second, a green reporter laser simultaneously excites a fluorescent dye bound to the labeled reporter molecule in the assay. The amount of green fluorescence is directly proportional to the amount of analyte (antibody) captured in the immunoassay (a quantitative analysis). 
     Digital signal processing algorithms, for example in the host computer or in the detector module, provide real-time data acquisition from thousands of beads per second. Using high speed digital signal processing, about 100,000 beads can be screened per minute and up to 25 different analytes (antibodies) can be assessed in seconds. Extrapolating the standard curve allows the quantitation of each analyte in the sample. 
     According to one embodiment, a MAD system essentially comprises two sub-systems, namely an assay processing sub-system (e.g., a sample processing module) and an analysis sub-system (e.g., a detector module). The assay processing sub-system includes, inter alia, the following hardware components: reaction vessels (RVs); RV handlers; an RV hopper; reagent kits; specimen and reagent handlers and probes; at least one bar-code reader; a specimen input area including a specimen rack positioned on a specimen rack tray; a look-ahead platform or pre-view area; a specimen robot; other robotics for transferring the samples and/or reagents; a reagent carousel; other carousels including sample racks; a work surface; an incubation wheel or carousel; at least one specimen aspiration probe; a washing mechanism, including a wash carousel and a wash aspiration robot; and a specimen cleaning station. Furthermore, the assay processing sub-system includes, inter alia, the following software components: software used to control and monitor processing, such as the maintenance sentry, instrument sentry, and sample sentry; a laboratory automation track system (LATS); a laboratory information system (LIS); quality control (QC) tools; remote connectivity management software; and user interfaces. 
     5.5.2 Serology IgG 
     In one example, serology infectious disease testing covers all areas of infectious disease, including sexually transmitted diseases, pediatric diseases, viral infections, parasitic infections and others. As an example, a system serology IgG reagent kit includes antigens for up to twelve or more specific infectious diseases. In this example, sixteen specific antigens are used for this purpose. Multiple antigens are used for specific disease association in order to increase assay specific reactivity, and to aid in the clinician diagnosis for staging of the specific disease. TABLE 19 provides of examples of the markers that may be included in a Serology IgG Reagent Kit. 
     
       
         
           
               
             
               
                 TABLE 19 
               
             
            
               
                   
               
               
                 Serology IgG Reagent Kit Markers 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                 ANTI- 
                   
               
               
                 DISEASE 
                 ANTIGEN 1 
                 ANTIGEN 2 
                 GEN 3 
                 COATING 
               
               
                   
               
               
                 Toxoplasmosis 
                 
                   T. gondii 
                 
                 None 
                 None 
                 Single 
               
               
                 Rubella 
                 Rubella 
                 None 
                 None 
                 Single 
               
               
                 Cytomegalovirus 
                 CMV 
                 None 
                 None 
                 Single 
               
               
                 Herpes Simplex 1 
                 HSV-1 
                 None 
                 None 
                 Single 
               
               
                 Herpes Simplex 2 
                 HSV-2 
                 None 
                 None 
                 Single 
               
               
                 Epstein Barr 
                 VCA 
                 EBNA-1 
                 EA-D 
                 Individual 
               
               
                 Virus 
               
               
                 Measles 
                 Measles 
                 None 
                 None 
                 Single 
               
               
                 Mumps 
                 Mumps 
                 None 
                 None 
                 Single 
               
               
                 Varicella 
                 VZV 
                 None 
                 None 
                 Single 
               
               
                 Zoster Virus 
               
               
                 Syphilis 
                 
                   T. pallidum 
                 
                 
                   T. pallidum 
                 
                 None 
                 Individual 
               
               
                   
                 r 15 
                 r 47 
               
               
                 Lyme 
                 
                   B. 
                 
                 
                   B. garinii 
                 
                 
                   B. afzelli 
                 
                 Individual 
               
               
                   
                 
                   burgaorferi 
                 
               
               
                   
                 31 
               
               
                 
                   Helicobacter 
                 
                 
                   H. pylori 1 
                 
                 
                   H. pylori 2 
                 
                 None 
                 Co-Coat 
               
               
                 
                   Pylori 
                 
               
               
                   
               
            
           
         
       
     
     The first column identifies disease. The second, third, and fourth indicate what antigens are used to detect the disease. The last column identifies how the antigens are coated. Single indicates only one antigen. Individual indicates multiple antigens for same disease, however the listed antigens are coated onto separate beads for identification. Co-Coat indicates multiple antigens coated on the same bead. 
     Diseases with more than one antigen can be a powerful tool to acquire clinical diagnosis of a sample. For example, EBV infection uses three IgG antigens to identify the disease stage and progression. Offering all three antigens in one tube will give more consistent results, and will offer “possible” disease stage progression, based on an internal look-up table. Syphilis uses two specific recombinant proteins to give higher sensitivity and specificity for a syphilis infection, and may offer disease staging “ideas” to the clinician based on pattern. Lyme offers three distinct strains of Borrelia in order to increase sensitivity, increase market usability, and other potential diseases progression “ideas” based on patterns.  H. pylori  uses two specific proteins 
     Referring to  FIGS. 49-51 , a method  900  according to the invention is illustrated utilizing the serology IgG assay panel as an example. Method  900  is shown in all three  FIGS. 49-51 , with the steps beginning at  920  of  FIG. 49  continued in  FIG. 50 , and the steps shown in  930  of  FIG. 900  continued in  FIG. 51 . It should, however, be appreciated that the sequence of steps or the combination of movements may be altered. The IgG assay panel of this example uses three reagents in the reagent packs—magnetic beads solution, sample diluent, and conjugate solution. Once a test run is completed and the instrument is in the idle phase, the MAD system automatically flushes at regular time intervals with wash buffer so as to prevent drying of the probes. The MAD system performs all of the assay steps without operator intervention. A single assay panel or multiple random-access assays can be performed with minimal operator time. 
     5.5.3 Serology IgM 
     Detection of IgM antibodies is often used to identify an early or acute infection and is helpful to fully understand the progression of an infection. 
     Serology IgM in some cases offers a few more challenges to antibody detection than IgG. Two main problems that can occur with IgM detection include IgG replacement and Rheumatoid Factor replacement. First, if a sample has both IgG and IgM antibodies to one antigen, the IgG antibody will always bind to the antigen first. The IgG and IgM antibodies compete for the same antigen, and IgG will almost always win, due to steric hindrances and higher affinity. This can lead to false negative results on a standard IgM assay. Second, Rheumatoid factor, a protein found in a large percent of the population, “mimics” IgM antibodies. Rheumatoid factor will bind to antigens non-specifically, leading to false positive results in the assay. A “capture method” immunoassay helps overcome these problems. 
     In this example, a capture method for IgM detection uses an IgM antibody coated to the solid phase. This IgM antibody will bind to a IgM in a sample. A conjugate, made up of the specific antigen for testing, is then added to the sample, and will bind to the complex. This then generates a signal that can be detected. 
     For a standard indirect IgM assay, an extra step is generally performed in order to remove all the IgG antibodies and all the Rheumatoid Factor from the sample. On manual or semi-automated assays, this can cause major delays and problems for programming. 
     The system  10  serology IgM reagent kit uses an indirect technique, with the absorption step included in the first incubation. The chemistry allowed within the multiplex format does not allow for “capture-like” tests to be developed. This serology IgM reagent kit has proven equivalence versus the capture methods where appropriate. 
     The serology IgM reagent kit offers essentially the same testing procedure and analyte package as Serology IgG described above, except that: 
     (a) EBV only offers VCA detection to IgM. Other markers are no value to determining disease stages and are not reimbursable. 
     (b) Syphilis still uses two distinct recombinant proteins, however the proteins used are  T. pallidum  17 and  T. pallidum  r 47. Advantages are still present using two distinct antigens. 
     (c)  H. pylori -only one antigen is used for detection. However, more may be used. 
     5.5.4 Autoimmune Systemic Reagent Kit 
     A MAD system  10  Autoimmune Systemic Reagent Kit offers antibody detection against antigens normally identified as systems autoimmune antigens. This indicates a response that is system-wide, throughout the whole body, and cannot be identified to one specific organ or organs. Disease specific panels affecting multiple organ systems will be used in future product launches. TABLE 20 includes a list of all the antigens present in a MAD System Autoimmune Reagent Kit according to one example. 
     
       
         
           
               
             
               
                 TABLE 20 
               
               
                   
               
               
                 Antigens in Autoimmune Reagent Kit 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                   
                 SSA 
               
               
                   
                 SSA 52 
               
               
                   
                 SSB 48 
               
               
                   
                 Sm BB 
               
               
                   
                 Sm 
               
               
                   
                 SM RNP 
               
               
                   
                 RNP 68 
               
               
                   
                 RNP A 
               
               
                   
                 Ribosomal P 
               
               
                   
                 Nucleosome (DNP) 
               
               
                   
                 dsDNA (quantitative) 
               
               
                   
                 Centromere B 
               
               
                   
                 Sci-70 
               
               
                   
                 Jo-1 
               
               
                   
                   
               
            
           
         
       
     
     Diseases associated with the above markers, including systemic lupus erythematosus, scleroderma, sjogrens synaroma polymyositis, mixed connective tissue disease (MCTD), and CREST, will not be discussed in detail herein, however they are know in the field. 
     Software on the M.A.D. system host computer  40  preferably allows the Autoimmune Systemic Reagent Kit to report results in many different methods. One standout feature with this embodiment is the incorporation of a medical decision device system. This system incorporates database in system memory  45  including results generated from known clinical disease samples. As new samples are tested on the system, the antibody response results for that sample are “compared” to the internal database. If the pattern of antibody response is similar to a known clinical disease, the system has the ability to report this correlation. 
     5.6 Functional Description of a MAD System 
       FIG. 52  is a block diagram providing a functional description of a MAD system  10 , depicting interrelationships of the various functions as described herein which may be performed by the system. 
     As used throughout this specification MAD and BioPlex2200 are or will be used as trademarks covering this device, processes of this device, and/or any part thereof. The use of MAD and BioPlex2000 is intended to be used in a distinctive sense, not a generic description of the system or method being accomplished. 
     The foregoing descriptions of specific embodiments of the present invention are presented for purposes of illustration and description. For example, any methods described herein are merely examples intended to illustrate one way of performing the invention. They are not intended to be exhaustive or to limit the invention to the precise forms disclosed. Obviously many modifications and variations are possible in view of the above teachings. Also, any graphs and FIGS. described herein are not drawn to scale. The embodiments were chosen and described in order to best explain the principles of the invention and its practical applications, to thereby enable others skilled in the art to best utilize the invention and various embodiments with various modifications as are suited to the particular use contemplated. Furthermore, the order of steps in the method is not necessarily intended to occur in the sequence laid out. It is intended that the scope of the invention be defined by the following claims and their equivalents.