Patent Publication Number: US-2019178903-A1

Title: Rotating sample positioning apparatus

Description:
This Application is a continuation of U.S. application Ser. No. 15/667,406, filed on Aug. 2, 2017, which is a continuation of U.S. application Ser. No. 14/922,892, filed on Oct. 26, 2015, now U.S. Pat. No. 9,753,047, issued on Sep. 5, 2017, which claims priority to U.S. Provisional Application No. 62/069,112, filed Oc. 27, 2014. 
    
    
     FIELD 
     The present application relates generally to sample analysis systems and, in particular, to a lateral flow cell positioning system for use in a sample-to-answer analysis system for detection of biological materials in a sample. 
     BACKGROUND 
     Molecular testing is a test designed to detect and identify biological materials, such as DNA, RNA and/or proteins, in a test sample. Molecular testing is beginning to emerge as a gold standard due to its speed, sensitivity and specificity. For example, molecular assays were found to be 75% more sensitive than conventional cultures when identifying enteroviruses in cerebrospinal fluid and are now considered the gold standard for this diagnostic (Leland et al., Clin. Microbiol Rev. 2007, 20: 49-78) 
     Molecular assays for clinical use are typically limited to identification of less than six genetic sequences (e.g., real-time PCR assays). Microarrays, which are patterns of molecular probes attached to a solid support, are one way to increase the number of sequences that can be uniquely identified. The microarray analysis workflow often includes an expensive scanner for extracting fluorescence intensity information from the microarray elements. Microarray imaging may show improved signal-to-noise ratios when water is removed from the microarray elements (i.e, when the microarray is dried). Therefore, there is a need for developing simpler, more efficient and more cost effective methods and devices for performing molecular tests using microarray technology. 
     SUMMARY 
     In one aspect, a Lateral Flow Cell (LFC) positioning system for a sample analysis device includes (1) a carousel comprising a platform and a sample loading tray mounted on the platform, and (2) a stage comprising a positioning system for positioning said carousel, wherein the sample loading tray is configured for holding a cartridge comprising one or more LFCs. In some embodiments, the carousel is movable relative to the stage. In other embodiments, the carousel is rotatable relative to the stage. 
     In other embodiments, the carousel further comprises a clamp comprising a top bar, a bottom bar and at least one supporting rod connecting the top bar and the bottom bar. The platform and the sample loading tray are disposed between the top bar and the bottom bar of the clamp. The clamp is movable relative to the platform and is capable of securing a cartridge in the sample loading tray when the clamp is moved to a locked position. 
     In certain preferred embodiments, the stage includes a motor-driven rotor connected to the carousel to facilitate its rotation. Rotation of the carousel translates to a cartridge containing LFCs with typical rotational velociities in the range upwards of 200 rpm (e.g., 200-5000 rpm). This centrifugal force drives the water droplets within the reaction chambers toward an absorbent, leaving the reaction chamber in a dry state. Thus, microarray elements, including bound and/or amplified probes are retained in a dry state. Following the drying procedure, the rotational velocity of the carousel decreases and enters an indexing mode for imaging. During this mode, each of the reaction chambers indexes into position under a microarray imaging camera. An image is acquired, processed and analyzed. Then, the test result is reported. 
     Another aspect relates to an integrated sample analysis system. The system includes a sample purification device comprising a monolith that binds specifically to nucleic acids; a sample analysis device comprising a reaction chamber comprising a hydrophilic interior surface configured to hold a microarray comprising a plurality of nucleic acid-based probes; a temperature control module comprising heating and cooling elements to enable thermal exchange between said heating and cooling elements and the internal volume of said reaction chamber; an imaging device positioned to capture an image of said microarray in said reaction chamber; and an LPC positioning module as described herein. 
     Further aspects include methods for rotating and/or positioning the carousel of the present invention and to methods for detecting and analyzing probes bound to the microarrays in the LFCs of the present invention. 
    
    
     
       BRIEF DESCRIPTION OF DRAWINGS 
       For the purposes of this disclosure, unless otherwise indicated, identical reference numerals used in different figures refer to the same component. 
         FIG. 1  is a diagram of an exemplary sample detection system of the present application. 
         FIGS. 2A-2B  depict an embodiment of a carousel for rotating lateral flow cells in a cartridge from a loading position ( FIG. 2A ) to an imaging position ( FIG. 2B ) under a microarray imaging system. 
         FIGS. 3A and 3B  show the top view ( FIG. 3A ) and bottom view ( FIG. 3B ) of the carousel, including the clamp, in  FIGS. 2A-2C . 
         FIGS. 4A-4B  depict another embodiment of a carousel for rotating LFCs in a cartridge from a loading position ( FIG. 4A ) to an imaging position ( FIG. 4B ) under a microarray imaging system. 
         FIG. 5  depict another embodiment of a carousel for rotating LFCs in a loading position. F 
         FIG. 6  depicts the embodiment of a carousel for rotating LFCs of  FIG. 5  in an imaging position under a microarray imaging system. 
         FIG. 7  show the carousel in  FIGS. 5 and 6 . 
         FIG. 8  shows the top of another carousel embodiment, including dual clamps for positioning a microarray in the field of view of an imager. 
         FIGS. 9A-9B  depict an embodiment of a positioning module for imaging microarrays comprising the carousel of  FIG. 8  for rotating a sample cartridge from a loading position ( FIG. 9A ) to a position for imaging ( FIG. 9B ). 
         FIGS. 10A-10C  show exemplary designs of LFC. 
         FIGS. 11A-11C  show exemplary cartridges, which includes a Lateral Flow Array (LFA), which is an array of LFCs. 
         FIG. 12  shows a control uniform array labeled with Cy3. 
         FIG. 13  shows a test Mycobacterium tuberculosis (TB) array imaged using the positioning module embodiment depicted in  FIGS. 9A-9B . 
         FIG. 14  shows processing of the array of  FIG. 13  using automated microarray analysis (AMA) software. 
         FIG. 15  shows an embodiment of a sample purification device of the present application. 
         FIGS. 16A and 16B  show embodiments of the heating and cooling device with LFCs resting on top of the heat spreader ( FIG. 16A ) or below the heat spreader ( FIG. 16B ). 
         FIGS. 17A-17C  show an embodiment of the optical subsystem. 
     
    
    
     DETAILED DESCRIPTION 
     The following detailed description is presented to enable any person skilled in the art to make and use the invention. For purposes of explanation, specific nomenclature is set forth to provide a thorough understanding of the present application. However, it will be apparent to one skilled in the art that these specific details are not inquired to practice the invention. Description of specific embodiments and applications is provided only as representative examples. This description is an exemplification of the principles of the invention and is not intended to limit the invention to the particular embodiments illustrated. 
     This description is intended to be read in connection with the accompanying drawings, which are considered part of the entire written description of this invention. The drawing figures are not necessarily to scale and certain features of the invention may be shown exaggerated in scale or in somewhat schematic form in the interest of clarity and conciseness. In the description, relative terms such as “front,” “back” “up,” “down,” “top” and “bottom,” as well as derivatives thereof, should be construed to refer to the orientation as then described or as shown in the drawing figure under discussion. These relative terms are for convenience of description and normally are not intended to require a particular orientation. Terms concerning attachments, coupling and the like, such as “connected” and “attached,” refer to a relationship wherein structures are secured or attached to one another either directly or indirectly through intervening structures, as well as both movable or rigid attachments or relationships, unless expressly described otherwise. 
     As used herein, the term “sample” includes biological samples such as cell samples, bacterial samples, virus samples, samples of other microorganisms, samples obtained from a mammalian subject, preferably a human subject, such as tissue samples, cell culture samples, stool samples, and biological fluid samples (e.g., blood, plasma, serum, saliva, urine, cerebral or spinal fluid, lymph liquid and nipple aspirate), environmental samples, such as air samples, water samples, dust samples and soil samples. 
     The term “monolith,” “monolith adsorbent” or “monolithic adsorbent material,” as used in the embodiments described herein, refers to a porous, three-dimensional adsorbent material having a continuous interconnected pore structure in a single piece. A monolith is prepared, for example, by casting, sintering or polymerizing precursors into a mold of a desired shape. The term “monolith” is meant to be distinguished from two or more filters that are placed next to each other or pressed against each other. The term “monolith adsorbent” or “monolithic adsorbent material” is meant to be distinguished from a collection of individual adsorbent particles packed into a bed formation or embedded into a porous matrix, in which the end product comprises individual adsorbent particles. The term “monolith adsorbent” or “monolithic adsorbent material” is also meant to be distinguished from a collection of adsorbent fibers or fibers coated with an adsorbent, such as filter papers or filter papers coated with an adsorbent. 
     The term “specifically bind to” or “specific binding,” as used in the embodiments described herein, refers to the binding of the adsorbent to an analyte (e.g., nucleic acids) with a specificity that is sufficient to differentiate the analyte from other components (e.g., proteins) or contaminants in a sample. In one embodiment, the term “specific binding” refers to the binding of the adsorbent to an analyte in a sample with a binding affinity that is at least 10-fold higher than the binding affinity between the adsorbent and other components in the sample. A person of ordinary skill in the art understands that stringency of the binding of the analyte to the monolith and elution from the monolith can be controlled by binding and elution buffer formulations. For example, elution stringencies for nucleic acids can be controlled by salt concentrations using KCl or NaCl. Nucleic acids, with their higher negative charge, are more resistant to elution than proteins. Temperature, pH, and mild detergent are other treatments that could be used for selective binding and elution. Thermal consistency of the binding and elution may be maintained with a heat block, water bath, infrared heating, and/or heated air directed at or in the solution. The manipulation of the binding buffer is preferable since the impact of the modified elution buffer on the downstream analyzer would need to be evaluated. 
     The term “nucleic acid,” as used in the embodiments described herein, refers to individual nucleic acids and polymeric chains of nucleic acids, including DNA and RNA, whether naturally occurring or artificially synthesized (including analogs thereof), or modifications thereof, especially those modifications known to occur in nature, having any length. Examples of nucleic acid lengths that are in accord with the present invention include, without limitation, lengths suitable for PCR products (e.g., about 50 to 700 base pairs (bp)) and human genomic DNA (e.g., on an order from about kilobase pairs (Kb) to gigabase pairs (Gb)). Thus, it will be appreciated that the term “nucleic acid” encompasses single nucleotides as well as stretches of nucleotides, nucleosides, natural or artificial, and combinations thereof, in small fragments, e.g., expressed sequence tags or genetic fragments, as well as larger chains as exemplified by genomic material including individual genes and even whole chromosomes. The term “nucleic acid” also encompasses peptide nucleic acid (PNA) and locked nucleic acid (LNA) oligomers. 
     The term “hydrophilic surface” as used herein, refers to a surface that would form a contact angle of 45.degree. or smaller with a drop of pure water resting on such a surface. The term “hydrophobic surface” as used herein, refers to a surface that would form a contact angle greater than 45.degree. with a drop of pure water resting on such a surface. Contact angles can be measured using a contact angle goniometer. 
     Sample-To-Answer Sample Analysis System  100   
     A principal aspect of the instant application relates to an LFC positioning module  130  for a sample-to-answer sample analysis system  100 .  FIG. 1  is a diagram of an exemplary sample analysis system  100 , which includes a sample processing module  110  containing a sample purification device, a temperature control module  120  containing a heating and cooling device, a detection module  140  containing a microarray imaging system, and an LFC positioning module  130  for positioning the LFCs into the field of view of the detection module  140  containing the microarray imaging system. 
     Sample Processing Module  110   
     The sample processing module  110  prepares a sample for analysis. Such preparation typically involves purification or isolation of the molecules of interest, such as DNA, RNA or protein, from the original sample using a sample purification device. The isolated molecules of interest are then transferred into the reaction chamber of an LFC. In some embodiments, the reaction chamber contains microarray for detection of the molecules of interest and a hydrophilic interior surface to facilitate the complete filling of the reaction chamber with an aqueous liquid. 
     In some embodiments, the sample purification device includes a monolith that binds specifically to nucleic acids. In certain embodiments, the sample purification device is a pipette tip containing a filter that binds specifically to the molecules of interest. Exemplary filters are further described in U.S. Pat. No. 7,785,869 and 8,574,923, both of which are incorporated by reference in their entirety. 
     In some other embodiments, the sample processing module  110  further comprises a cell lysis chamber having a plurality of cell lysis beads and a magnetic stirrer. Cell lysis is achieved by rotating the magnetic stirrer inside the cell lysis chamber in the presence of the cell lysis beads. The rotation of the magnetic stirrer is created by an alternating magnetic field induced by the rotation of north and south poles of a magnet, which is external to the tube. In some embodiments, the magnet is a cylinder shaped magnet. The magnet rotates about an axis A and causes a magnet stir element in the chamber to rotate in the same direction along an axis B that is parallel to axis A. The rotating magnetic stir element collides with beads, which lyse cells in the process. The magnet may be positioned alongside, above, below or diagonally from the chamber. In some embodiments, a cylinder shaped magnet is rotating about an axis that is parallel to a surface that the cell lysis chamber is placed on. The cell lysis beads can be any particle-like or bead-like material that has a hardness greater than the hardness of the cells to be lysed. The cell lysis beads may be made of plastic, glass, ceramics, or any other non-magnetic materials, such as non-magnetic metal beads. In certain embodiments, the cell lysis beads are rotationally symmetric to one axis (e.g., spherical, rounded, oval, elliptic, egg-shaped, and droplet-shaped particles). In other embodiments, the cell lysis beads have polyhedron shapes. In other embodiments, the cell lysis beads are irregular shaped particles. In yet other embodiments, the cell lysis beads are particles with protrusions. The magnetic stirrer can be a bar-shaped, cross-shaped, V-shaped, triangular, rectangular, rod or disk-shaped stir element, among others. In some embodiments, the magnetic stirring element has a rectangular shape. In some embodiments, the magnetic stirrer has a two-pronged tuning fork shape. In some embodiments, the magnetic stirrer has a V-like shape. In some embodiments, the magnetic stirrer has a trapezoidal shape. In certain embodiments, the longest dimension of the stir element is slightly smaller than the diameter of the container (e.g. about 75-95% of the diameter of the container). In certain embodiments, the magnetic stirrer is coated with a chemically inert material, such as polymer, glass, or ceramic (e.g., porcelain). In certain embodiments, the polymer is a biocompatible polymer such as PTFE and parylene. A more detailed description of the magnetic lysis method is described in application Ser. No. 12/886,201, which is hereby incorporate by reference. 
     Temperature Control Module  120 . 
     The temperature control module  120  controls the temperature of the reaction chamber during amplication and/or binding reactions. In certain embodiments, the temperature control module comprises a heating and cooling device with a flexible temperature control surface, as described in U.S. Pat. Nos. 7,955,840 and 7,955,841, both of which are hereby incorporated by reference in their entirety. In other embodiments, the temperature control module  120  employs a heating and cooling device with a hard, flat temperature control surface as described in U.S. patent application Ser. No. 14/743,389, filed Jun. 18, 2015, the teachings of which are expressly incorporated by reference herein. 
     In some embodiments, the temperature control module  120  includes a thermoelectric device. One or more thermoelectric devices can be integrated into the module. In other embodiments, the temperature control module  120  further comprises a temperature sensor. Examples of temperature sensors are resistance thermal devices (RTDs), thermocouples, thermopiles, and thermistors. 
     In some embodiments, the thermoelectric device is a Peltier device made of ceramic materials. Examples of ceramic materials include: alumina, beryllium oxide, and aluminum nitride. 
     In other embodiments, the thermoelectric device is a thin film semiconductor (e.g., bismuth telluride). In other embodiments, the thermoelectric de vice is a thermoelectric couple made of p and n type semiconductors. Examples of p and n type semiconductors are bismuth antimony, bismuth telluride, lead telluride, and silicon germanium. 
     In some embodiments, the thermoelectric device has a heat sink coupled to one side and a heat spreader coupled to the other side. Examples of heat sinks and heat spreaders are copper, aluminum, nickel, heat pipes, and/or vapor chambers. During operation, the heat spreader makes intimate contact with an exterior surface of the reaction chamber and controls the temperature inside the reaction chamber. In some embodiments, the heat sink and/or heat spreader are coupled to the thermoelectric device with thermally-conductive epoxy, thermally-conductive adhesives, liquid metal (e.g., gallium) or solder (e.g., indium). In some embodiments, the temperature control module  120  further comprises a fan under the heat sink. In one embodiment the heat spreader is flat. In some of these embodiments the heat spreader is rectangular with dimensions that range from 3 mm.times.3 mm to 20 mm.times.20 mm. The thickness of the heat spreader is preferably 0.05 to 5 mm, and more preferably 0.1 to 0.5 mm, and even more preferably 0.15 to 0.3 mm. 
     LFC Positioning Module  130   
     The LFC positioning module  130  positions the LFC for detection of signals in the microarray by the detection module  140 . In one aspect, the LFC positioning module includes (1) a carousel comprising a platform and a sample loading tray mounted on the platform, and (2) a stage comprising a positioning system for positioning the carousel. The sample loading tray is configured for holding a cartridge comprising one or more LFCs. In some embodiments, the carousel is movable relative to the stage. In some embodiments, the LFC positioning module  130  is configured to allow heating and cooling of LFCs in the sample loading tray by the temperature control module  120 , and real time monitoring of a reaction in the reaction chamber of a LFC by the detection module  140 . In other embodiments, the carousel is rotatable e relative to the stage. In other embodiments, the carousel is capable of spinning to remove liquid from a reaction chamber of an LFC. 
     In other embodiments, the carousel further comprises a clamp having a top bar, a bottom bar and at least one supporting rod connecting the top bar and the bottom bar. The platform and the sample loading tray are disposed between the top bar and the bottom bar of the clamp. The clamp is movable relative to the platform and is capable of immobilizing a cartridge in the sample loading tray when the clamp is moved to a locked position. 
     In other embodiments, the positioning module  130  contains a built-in heating and cooling device that is capable of heating and cooling the LFC(s) in the cartridge. In other embodiments, the carousel is movable to a reaction position to bring the cartridge into contact with a heating and cooling device to facilitate reactions in the reaction chamber of an LFC within the cartridge. In some embodiments, the heating and cooling device is configured to allow real-time monitoring of a reaction within the reaction chamber of the LFC by the detection module  140 . 
     In certain embodiments, the stage includes a motor-driven rotor connected to the carousel to facilitate its rotation. Rotation of the carousel sets in rotational motion a cartridge containing an LFC. This centrifugal force drives the water droplets within reaction chambers toward an absorbent, leaving the reaction chamber in a dry state. Thus, microarray elements, including bound and/or amplified probes are retained in a dry state. Following the drying procedure, the rotational velocity of the carousel decreases and enters an indexing mode for imaging. During this mode, each of the reaction chambers indexes into position under a microarray imaging camera. An image is acquired, processed and analyzed. Then, the test result is reported. 
     In an embodiment shown in  FIGS. 2A-2B , the LFC positioning module  130  includes a stage  142  and a rotatable carousel  144 . The rotatable carousel  144  comprises a platform  145  with a sample loading tray  152  that holds a cartridge  146  comprising a single LFC. The carousel  144  is connectively linked to a clamp  150  that immobilizes the cartridge  146  in the sample loading tray  152  in a locked position, and allows the removal of the cartridge  146  from the sample loading tray  152  or insertion of the cartridge  146  into the sample loading tray  152  in an open position. In this embodiment, the clamp  150  contains two supporting rods  154  connected to a top bar  156  and bottom bar  158  as part of the platform  145 . The outwardly extending handle  162  is attached to the platform  145  to facilitate rotation or indexing of the carousel  144  from a loading position ( FIG. 2A ) to an imaging position ( FIG. 2B ). 
       FIG. 3A  is a top view of the carousel  144 , showing the platform  145 , a handle  162 , the sample loading tray  152 , the cartridge  146  and the top bar  156  of the clamp  150 .  FIG. 3B  is a bottom view of the carousel  144 , including the bottom bar  158  and the supporting rods  154 . The sample tray  152  resides in the carousel  144  between the top and bottom bars  156 ,  158 . The sample loading tray  152  remains in a fixed position while the clamp  150  translocates up or down, locking the cartridge  146  in the sample loading tray  152  at the down position (locked position) and allowing the cartridge  146  to be inserted into, or removed from, the sample loading tray  152  at the up position (open position). A magnet  160  may be placed at the bottom side of the platform  145  for releasable attachment to the bottom bar  158  to keep the clamp  150  at an open position. 
     In some embodiments, a motor-driven rotor (not shown) is disposed within the stage  142  for rotating the carousel  144  holding the disposable cartridge  146 . The rotor rotates the carousel  144  and cartridge  146  at rotational velocities producing centrifugal forces sufficient to drive water droplets from reaction chambers in the LFCs  148  toward an absorbent  62  in a waste chamber  60  therein ( FIG. 10A ), drying the LFC  148  so as to enhance the imaging of nucleic acids or proteins bound to microarrays in the LFCs  148 . Exemplary motors for rotating the carousel  144  include a stepper motor, a servo motor and a DC motor. In one embodiment the rotor rotates the carousel at rotational velocities of at least 200 rpm, at least 300 rpm, at least 500 rpm, at least 1000 rpm; between about 200 to 5000 rpm, between 200 to 2500 rpm, between 250 to 1000 rpm, or between 400 to 800 rpm. 
     Upon completion of the drying process, the rotational velocity of the carousel  144 /cartridge  146  decreases, whereupon the drying/positioning module enters an indexing mode for imaging. During this mode, each of the microarrays is indexed into position under a microarray imaging camera in the detection module  140 . Specifically, the carousel  144  is indexed into position so that a desired microarray enters the field of view for imaging. Images of biomolecule binding results are acquired, processed, analyzed and reported. 
     In some embodiments, including  FIGS. 2A-2B , the stage  142  includes an “XYZ positioner system” comprising knobs  166 ,  168 ,  170  for positioning the LFCs in appropriate positions for imaging. Actuating the knobs  166 ,  168 ,  170  enables the user to vary the position of the microarrays in the x, y, z axes for imaging bound biomolecules in the reaction chamber  10  and/or microarrays  40  therein (see e.g.,  FIG. 10A ). Additionally, in some embodiments, an angular adjustment micrometer  171  is employed to adjust the tilt or yaw angle of the platform  145 . Once the sample tray is properly located under the camera for imaging, the positions of the X and Y stages are locked in place, for example by set screws such as the Y stage locking screw  172  depleted in  FIG. 2B . In some embodiments, a platform locking screw  173  prevents rotation of the platform  145  when in the imaging position. 
       FIGS. 4A-4B  depict another embodiment of a carousel  144  for rotating LFCs in a cartridge from a loading position ( FIG. 4A ) to an imaging position ( FIG. 6 )  4 B under a microarray imaging system. 
       FIGS. 5 and 6  depict another embodiment of a carousel for rotating LFCs in a cartridge from a loading position ( FIG. 5 ) to an imaging position ( FIG. 6 ) under a microarray imaging system. 
       FIG. 7  shows the carousel  144  in  FIGS. 5 and 6 . 
       FIGS. 8 and 9A-9B  show an embodiment of a positioning module for microarray imaging comprising a state  142  and a rotatable carousel  144 . It is understood that different elements of each embodiment of the microarray imaging positioning module can be used interchangeably as practicably allowed. 
       FIG. 8  shows the carousel  144  with the attached sample loading tray  152 . The sample loading tray  152  has two independent clamp  150  that can be slide up and down the Z axis. The clamps  150  each contains a top bar or bracket  180  and a bottom bar  158 . When the clamp  150  is in a lifted position, the bottom bar  158  is held in place by a magnetic latch to facilitate sample loading with the same mechanism as shown in  FIG. 3B . The sample loading tray  152  can be used with cartridges  146  comprising different formats of microarray packaging—from standard 1″.times.3″ glass or plastic substrates with microarrays printed on them to microarrays encapsulated into a microfluidic flow cell that may have complex thickness profiles due to such features as sealable inlet port and/or integral waste chambers. Non-limiting examples of LFC  148  and cartridge  146  are depicted in  FIGS. 10 and 11 . Because of their low-profile design, the clamping brackets do not block the excitation beam propagating at an oblique angle, which virtually eliminates restrictions on the position of microarray on the substrate. In some embodiments, the low profile design allows an oblique angle of view from the vertical of the microarray on the substrate of at least about 70 degrees. In other embodiments, the angle of view is at least about 75, 80 or 85 degrees. In still other embodiments, the angle of view is at least about 87.5 degrees. 
       FIGS. 9A-B  show a positioning device for microarray imaging comprising a stage  142  and a rotatable carousel  144  with the carousel in the sample loading and imaging positions. In  FIG. 9A , the carousel  144  is turned so that the sample loading tray  152  is in the sample loading position with the clamps  150  lifted and the magnetic latches engaged with the bottom bar  158 . Once the sample cartridge  146  is loaded, the magnets are disengaged with the bottom bar  158  by pushing the top bar or bracket  180  of the clamp  150  down. The weight of the top bar or bracket  180  and the bottom bar  158  holds the clamp  150  down to secure the sample cartridge  146  in place. 
       FIG. 9B  shows the controls in one embodiment of a stage  142  of a positioning device for microarray imaging, with the sample loading tray  152  moved into the imaging position. In some embodiments, the carousel  144  is locked with the sample loading tray  152  in the imaging position using a locking screw  173 . The fine location of the microarray within the sample cartridge  146  when the sample loading tray  152  is in the imaging position both by an angular adjustment micrometer  171 , which adjusts the angle of the rotary table comprising the carousel  144  and the sample loading tray  152  elements, as well as X, Y and Z axis controls incorporated into the stage  142 . In this embodiment, the stage  142  comprises an X axis translation stage  182  for sample positioning along the X axis and an X axis positioning knob  184  for adjusting the movement and an X axis lock  186  for fixing the position of the X axis stage  182 , allowing stable reproducible operation of the instrument&#39;s imaging system. In some embodiments, the X axis translation stage  182  comprises a rack-and-pinion mechanism for movement. In other embodiments, the X axis translation stage  182  comprises a worm gear or other suitable mechanism for movement. Also, in some embodiments, the X axis lock  186  comprises a lever mechanism that, when actuated, prevents the turning of the X axis positioning knob  184 . In other embodiments, the X axis lock  186  comprises a set screw mechanism that, when engaged, contacts with and prevents the movement of the X axis translation stage  182 . In some embodiments, the X axis translation stage  182  has a range of motion of at least 25 mm in each direction from center. In other embodiments, the X axis translation. stage  182  has a range of motion of at least 30 or 35 mm in each direction from center. In still other embodiments, the X axis translation stage  182  has a range of motion of at least  40  mm in each direction from center. 
       FIG. 9B  further depicts the stage  142  of this embodiment of a microarray imagery positioning device comprises a Y axis translation stage  188  for sample positioning along the Y axis and a Y axis positioning knob  168  for adjusting the movement and a Y axis lock  172  for fixing the position of the Y axis translation stage  188 . In some embodiments, the Y axis translation stage  188  comprises a rack-and pinion mechanism for movement. In other embodiments, the Y axis translation stage  188  comprises a worm gear or other suitable mechanism for movement. In some embodiments, the Y axis lock- 172  comprises a set screw where mechanism that, when engaged, contacts with and prevents the movement of the Y axis transition stage  188 . In some embodiments, the Y axis translation stage  188  has a range of motion of at least 5 mm in each direction from center. In other embodiments, the Y axis translation stage  188  has a range of motion of at least 10, 15 or 20 mm in each direction from center. In still other embodiments, the Y axis translation stage  188  has a range of motion of at least 25 mm in each direction from center. 
     Also shown in  FIG. 9B , the stage also comprises a mechanism for Z axis control  170 , in order to focus the microarray under the imaging device. In some embodiments, the Z axis control  170  is a thumbwheel. In other embodiments, the Z axis control  170  is a lever or other suitable mechanism for fine-scale adjustment of the Z axis for proper focus. 
     In some embodiments, the positioning device for microarray imaging embodiment shown in  FIGS. 9A-9B  is a component of a microarray imaging system further comprising an imaging device. In some further embodiments the imaging device is a camera. 
     In some embodiments the array imaging system further comprises an excitation energy source. The excitation energy source is focused on the microarray being imaged by the imaging device. In some further embodiments, the excitation energy source is tunable for the wavelengths emitted. In other further embodiments, the excitation energy source emits multiple wavelengths simultaneously. In some embodiments, the excitation energy strikes the array at an oblique angle. In some embodiments, the array imaging system is enclosed in a light-tight enclosure. In some embodiments, the array imaging system is sized to fit on the top of a lab bench along with a computer for data analysis. 
     In some embodiments, the sample cartridge comprises a microarray immobilized to a glass slide. In other embodiments, the sample cartridge comprises a microarray immobilized to a polymer-based slide. In some embodiments, the microarray is printed onto the glass or polymer-based slide. In some embodiments, multiple microarrays are immobilized to or printed onto the glass or polymer-based slide. In other embodiments, each microarray is enclosed within an LFC. 
     In some embodiments, the cartridge  146  contains a single LFC  148 .  FIG. 10A  depicts an exemplary LFC  148 . The LFC  148  comprises a reaction chamber  10 , a waste chamber  60  and a channel  12  connecting the reaction chamber  10  to the waste chamber  60 . The reaction chamber contains a microarray  40 . The microarray  40  contains a plurality of attached probes for detection of nucleic acids or proteins. In some embodiments, the waste chamber  60  includes a liquid-retaining absorbent  62 . Two additional LFC designs are shown in  FIGS. 10B and 10C . 
     The microarray  40  can be a polynucleotide array or a protein/peptide Array. In one embodiment, the microarray  40  is formed by printing gel spots as described in e.g., U.S. Pat. Nos. 5,741,700, 5,770,721, 5,981,734, 6,656,725 and U.S. patent application Ser. Nos. 10/068,474, Ser. No. 11/425,667 and Ser. No. 11/550,730, all of which are hereby incorporated by reference in their entirety. 
     The reaction chamber  10  has a plurality of interior surfaces including a bottom surface on which the microarray  40  is formed and a top surface that faces the bottom surface and is generally parallel to the bottom surface. In some embodiments, at least one of the plurality of interior surfaces is a hydrophilic surface that facilitate the complete filling of the reaction chamber  10 . In one embodiment, the top surface of the reaction chamber  10  is a hydrophilic surface. Exemplary flow cell devices and embodiments are described in U.S. Pat. Nos. 8,680,025 and 8,680,026, which are expressly incorporated by reference in their entirety. 
     In other embodiments, the cartridge  146  contains LFCs  148 . The cartridge  146  may contain one or more LFCs  148 . In some embodiments, the cartridge  146  contains a unitary multi-microarray strip containing between 2 to 16 LFCs, between 4 to 12 LFCs or between 6-10 LFCs. In certain embodiments, the LFCs are shaped like wedges.  FIG. 11A  depicts a cartridge  146  with eight LFCs  148 . The cartridge  146  is attached to a manifold  1100  ( FIG. 11B ) that controls liquid flow within the LFCs  148 . Each LFC  148  contains a reaction chamber  1020  and each reaction chamber  1020  contains a microarray  1010 . The reaction chambers  1020  are configured for allowing reagents, such as PCR reagents to interact with the microarrays  1010 . By way of example, the manifold  1100  may direct reagents (e.g., PCR mixtures) pipetted in from a microtiter plate to the LFC  148  through dome valves  1120 , which also act as a seal during thermal cycling preventing any leakage, and pin valves  1130 , which are controlled by a linear actuator that enables them to be opened and closed. In an open position, the pin valves  1130  allow liquid flow during the wash steps. In a closed position, the pin valves  1130  help trap the reagents in the reaction chamber  1010  of the LFC  148  during e.g., thermal cycling. The absorbent  1140  attached to the manifold  1100  collects all wash buffers once passed through the LFC  148 .  FIG. 11C  shows another design of a multi-chamber cartridge. In this design, multiple reaction chambers  10  share a single waste chamber  60 . 
     Detection Module  140   
     The detection module  140  detects the presence of the molecules of interest in the reaction chamber. In some embodiments, the molecules of interest comprise the reaction product of an amplification reaction, such as a polymerase chain reaction (PCR). In certain embodiments, the detection module  140  comprises an optical subsystem designed to capture images of the microarray in the reaction chamber. In certain embodiments, the optical subsystem is specifically designed for low-level fluorescence detection on microarrays. The optical subsystem uses confocal or quasi-confocal laser scanners that acquire the microarray image pixel by pixel in the process of interrogating the object plane with a tightly focused laser beam. The laser scanners offer the advantages of spatially uniform sensitivity, wide dynamic range, and efficient rejection of the out-of-focus stray light. In some embodiments, the detection module  140  is capable of real time monitoring of the amplification reaction in the reaction chamber of a LFC. In certain embodiments, the detection module  140  comprises an optical subsystem with a laser light source. 
     In another embodiment, the optical subsystem uses imaging devices with flood illumination, in which all of the microarray elements (features) are illuminated simultaneously, and a multi-element light detector, such as a CCD camera, acquires the image of microarray either all at once or in a sequence of a few partial frames that are subsequently stitched together. Compared to laser scanners, CCD-based imaging devices have simpler designs and lower cost. CCD-based imaging systems are an attractive option for both stand-alone and built-in readers in cost-sensitive applications relying on microarrays of moderate complexity (i.e., having a few hundred or fewer array elements). Commercial instruments typically use cooled CCD cameras and employ expensive custom-designed objective lenses with an enhanced light-collection capability that helps to balance, to some extent, the low efficiency of the excitation scheme. 
     In another embodiment, the optical subsystem contains an imaging device that uses a non-cooled CCD camera. Although non-cooled cameras typically have a noticeably higher dark current as compared to the cooled models, the optical subsystem could provide the required sensitivity without using exposures is excess of a few seconds by (1) increasing the excitation intensity, or (2) employing an objective lens with high light collection efficiency; or (3) using the above two approaches in combination. The light source can be a conventional light source, such as a metal halide or mercury bulb, a laser-based system, or a high-intensity LED. 
     In another embodiment, the optical subsystem has a fluorescence-independent imaging (FII) mode as a supplementary imaging mode of microarray reader operation. The FII mode allows imaging the array elements regardless of their fluorescence level. 
     The practical implementation of FII is technically challenging in both microarray scanners and imagers using flood illumination. The problem is especially difficult when the microarrays to be imaged are the mainstream planar arrays, because the layer of biomolecular probes immobilized on the microarray substrate is too thin to produce a noticeable change in the intensity of light used for probing the slide surface. 
     In one embodiment, the present invention uses dark field illumination in reflected light for imaging gel arrays printed on opaque (black) plastic substrates. In another embodiment, the present invention uses oblique illumination in transmitted light for imaging gel arrays printed on transparent (glass) slides. In both cases, the light source used for FII could be any light source emitting within the transmission band of the imager&#39;s emission filter. 
     EXAMPLES 
     Example 1 
     Analysis of Arrays 
     In order to test the sample handling and imaging of the microarray imaging positioning device disclosed herein, a series of test arrays were printed. Briefly, the following steps were used for printing the test microarrays: (1) an oligonucleotide mixture was prepared and dried down on a CentriVap. (2) A copolymer solution comprising monomer, cross-linker, glycerol and buffer was prepared. (3) The dried oligonucleotide was dissolved in the copolymer solution. (4) The oligonucleotide-copolymer solution was placed into a source plate, and (5) the source plate was used for array printing/polymerization/washing. 
       FIG. 12  shows a uniform 12.times.18 microarray labeled with identical concentrations of cyanine Cy3 dye. The array was imaged using the microarray imaging positioning device comprising a stage and a rotatable carousel depicted in  FIGS. 9A-9B . 
       FIG. 13  shows an image of a Mycobacterium tuberculosis (MTB) microarray printed on a substrate as a component of an LFC. The MTB microarray is imaged with the positioning device for microarray imaging comprising a stage and a rotatable carousel depicted in  FIGS. 5A-9B . In this case, the capture instrument was running Akonni AMA software. 
       FIG. 14  shows the array of  FIG. 13  after processing by Akonii AMA software. The superimposed grid shows the results of automated spot detection, wherein a circle within a grid indicates the location of a microarray spot. 
     Example 2 
     Sample Purification Device 
       FIG. 15  shows an embodiment of a sample purification device  200  that includes a housing  210  and a sample filter  220 . The housing  210  defines a sample passageway  212  between a first opening  214  and a second opening  216 . The shape and size of the housing  210  are not particularly limited. In this embodiment, the preferred housing configuration is substantially cylindrical so that the flow vectors during operation are substantially straight. In the embodiment shown in  FIG. 15 , the housing  210  has a pipette tip geometry, i.e., the first opening  214  has a diameter that is greater than the diameter of said second opening  216 , and the first opening  214  is dimensioned to fit onto the tip of a pipette. 
     The sample filter  220  is placed in the close proximity of the second opening  216  so that samples are filtered immediately after being taken into the housing  210  through the second opening  216 . In one embodiment, the sample filter  220  is contiguous with the second opening  216 . In another embodiment, the sample filter  220  is separated from the second opening  216  by a distance of 1-20 mm. In some embodiments, the monolith sample filter is a glass frit with an average pore size of 20-200 micron. In another embodiment, the sample filter  220  is a monolith filter with two sections having different porosities: a first section at the proximity of the second opening  216  and a second section that is separated from the second opening  216  by the first section  221 . In one embodiment, the first section has an average pore size of 40-200 micron, preferably 40-60 micron, and the second section has an average pore size of 1-40 micron, preferably 1-20 micron. 
     Example 3 
     Heating and Cooling Device 
       FIGS. 16A-16B  show an embodiment of a heating and cooling device  300  in the temperature control module  120 , which provides both heating and cooling functions based upon switching the current. In some embodiments, the cartridge  146  disengages from the heating and cooling device  300  before centrifugal drying and imaging. In other embodiments imaging occurs simultaneously with heating or cooling to allow real-time monitoring e.g., nucleic acid amplification in the reaction chamber. The heating and cooling device  300  includes one or more heat spreaders  310  that are adapted to make contact with an exterior surface of the reaction chamber  10  of the LFC  148 , and one or more thermoelectric devices. In some embodiments, the thermoelectric device is a Peltier device made of ceramic materials, which provides both heating and cooling functions based upon switching the current. In other embodiments, the thermoelectric device is a thin film semiconductor (e.g., Bismuth Telluride), which provides both heating and cooling functions based upon switching the current. In other embodiments, the thermoelectric device is a thermoelectric couple made of p and n type semiconductors, which provides both heating and cooling functions based upon switching the current. 
     In some embodiments, the thermoelectric device has a heat sink coupled to one side and a heat spreader coupled to the other side. Exemplary heat sinks and heat spreaders include copper, aluminum, nickel, heat pipes, and/or vapor chambers. During operation, the heat spreader makes intimate contact with an exterior surface of the reaction chamber and controls the temperature inside the reaction chamber. In some embodiments, the heating-and-cooling module further comprises a fan under the heat sink. In one embodiment the heat spreader is flat. In some of these embodiments the heat spreader is rectangular with dimensions that range from 3 mm.times.3 mm to 20 mm.times.20 mm. The thickness of the heat spreader is preferably 0.05 to 5 mm, and more preferably 0.1 to 0.5 mm, and even more preferably 0.15 to 0.3 mm. 
     In some embodiments, the heating and cooling device  300  further comprises a temperature sensor. Exemplary temperature sensors include resistance thermal devices (RTDs), thermocouples, thermopiles, and thermistors. 
     In some embodiments, the LFCs  148  are located on top of the heat spreader ( FIG. 16A ). In some embodiments the heat spreader absorbs light. Examples of how to achieve light absorption include painting the heat spreader black, black anodizing, or coating it with black chrome. Light absorption reduces scatter that can interfere with imaging microarrays. In some embodiments, thermocycling occurs prior to imaging. In some embodiments thermocycling occurs simultaneously with imaging. 
     In other embodiments, the LFCs  148  are located below the heat spreader  310 . The heat spreader  310  is adapted to descend onto the reaction chamber  10  of the LFC  148  ( FIG. 16B ). Alternatively, the platform  320  may ascend to bring the LFC  148  in contact with the heat spreader  310 . 
     In other embodiments two or more heat spreaders interface with each reaction chamber. An example of this is that one heat spreader interfaces with the top of the reaction chamber while another heat spreader interfaces with the bottom of the reaction chamber. 
     Example 4 
     Optical Subsystem with Oblique Angle Illumination 
       FIGS. 17A-17C  show an embodiment of an optical subsystem with oblique angle illumination for microarray imaging schemes.  FIG. 17A  shows the general concept of oblique angle illumination for microarray imaging. The system&#39;s optical train comprises two separate channels  1210  and  1220 . Channel  1220  is used for fluorescence excitation and channel  1210  is used for imaging the array.  FIG. 17B  is an embodiment of the illumination optical train that includes a mirror to divert the illumination source at a 90 degree angle to allow a significant portion of the illumination optics to be parallel to the microarray substrate.  FIG. 17C  is an embodiment of the collection light optical train that includes a mirror to divert the collection light at a 90 degree angle to allow a significant portion of the detection optics to be parallel to the microarray substrate. 
     As shown in  FIGS. 17B and 17C , the optical train includes high-quality imaging optics (an objective lens  1230  and a matching video lens  1240 ), a compact low-noise monochrome ⅓″ CCD camera  1250 , and a 530 nm high-intensity LED as a fluorescence excitation source  1260 . In contrast to the commonly-used fluorescence microscopy epi-illumination scheme, in which the objective is used for both illuminating and imaging the object, this design eliminates the background due to both the excitation light back-scattered in the objective and the possible optics auto-fluorescence. Also, oblique illumination at a 45.degree. incidence angle helps to direct the major portion of the excitation light reflected from the microarray substrate away from the objective lens. Since the objective is infinity-corrected, the array surface of the slide should be positioned at the front focal plane of the lens. The emission filter  1255  is located in the infinity space between the objective and video lens and two-component beam expander comprising a plano-concave lens  1265  and an achromatic doublet  1270 . The beam expander (not shown) reduces the magnification factor of the entire lens system to 0.75.times. With the current CCD sensor having ⅓″ format and a 7.4 pm pixel size, this magnification adjustment allows imaging a microarray with up to 12.times.18 gel elements at a spatial resolution (limited by the CCD array pixel size) of about 10 .mu.m. The fluorescence excitation channel implements the Kohler illumination scheme for a projection system, which ensures uniform (within 3%) illumination of the object plane despite the complex structure of light emitting region of the LED. The bandpass cleanup filter placed between the collector and condenser lenses cuts off long-wavelengths of the LED emission spectrum that overlaps with the fluorescence band of Cy3. In some embodiments, the optical subsystem is configured to allow real-time imaging of a microarray in a reaction chamber. 
     The above description is for the purpose of teaching the person of ordinary skill in the art how to practice the present invention, and it is not intended to detail all those obvious modifications and variations of it which will become apparent to the skilled worker upon reading the description. It is intended, however, that all such obvious modifications and variations be included within the scope of the present invention, which is defined by the following claims. The claims are intended to cover the components and steps in any sequence which is effective to meet the objectives there intended, unless the context specifically indicates the contrary.