Abstract:
A multi-modal data acquisition system for detecting target material on a biological reaction surface, the system comprising a radiation source for generating an incoming beam that impinges on the biological reaction surface at an oblique incidence angle and produces a reflected beam, an interferometric detector for detecting an interferometric signal from the illuminated surface, the reflected beam being directed to the interferometric detector, a fluorescence detector for detecting a fluorescence signal from the illuminated surface; the fluorescence detector being positioned to substantially minimize the incidence of the reflected beam; and a processing system for receiving the interferometric and fluorescence signals and determining the presence or absence of target material on the biological reaction surface. A reaction surface conditioned for the simultaneous collection of fluorescence, interferometric and other signals. A multi-modal data acquisition system for collecting and processing additional modes, including multiple interferometric, fluorescence and scattering channels.

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
       [0001]    This application claims priority to U.S. Provisional Application Ser. No. 60/885,698, filed on Jan. 19, 2007, entitled “Four Channel Optical Detection on Protein-Patterned Biological Compact Disk” and to U.S. Provisional Application Ser. No. 60/916,177, filed on May 4, 2007, entitled “System with Extended Range of Molecular Sensing Through Integrated Multi-Modal Data Acquisition” the disclosures of which are both incorporated herein by this reference. 
         [0002]    This application is related to U.S. application Ser. No. 11/675,359, filed on Feb. 15, 2007, entitled “In-Line Quadrature and Anti-Reflection Enhanced Phase Quadrature Interferometric Detection”; U.S. patent application Ser. No. 10/726,772, entitled “Adaptive Interferometric Multi-Analyte High-Speed Biosensor,” filed Dec. 3, 2003 (U.S. Pat. Pub. No. 2004/0166593); U.S. Pat. No. 6,685,885, entitled “Bio-Optical Compact Disk System,” filed Dec. 17, 2001 and issued Feb. 3, 2004; U.S. patent application Ser. No. 11/345,462 entitled “Method and Apparatus for Phase Contrast Quadrature Interferometric Detection of an Immunoassay,” filed Feb. 1, 2006 (U.S. Pat. Pub. No. 2007/0003436); U.S. patent application Ser. No. 11/345,477 entitled “Multiplexed Biological Analyzer Planar Array Apparatus and Methods,” filed Feb. 1, 2006 (U.S. Pat. Pub. No. 2007/0003925); U.S. patent application Ser. No. 11/345,564, entitled “Laser Scanning Interferometric Surface Metrology,” filed Feb. 1, 2006 (U.S. Pat. Pub. No. 2006/0256350); U.S. patent application Ser. No. 11/345,566, entitled “Differentially Encoded Biological Analyzer Planar Array Apparatus and Methods,” filed Feb. 1, 2006 (U.S. Pat. Pub. No. 2007/0023643), the disclosures of which are all incorporated herein by this reference. 
     
    
     BACKGROUND AND SUMMARY OF THE INVENTION 
       [0003]    The present invention generally relates to an apparatus capable of simultaneous acquisition of data from multiple molecular sensing modalities, for example and not by way of limitation, a labeled process (such as a fluorescence process) and a label-free process (such as an interferometric process). 
         [0004]    Generally, labeled and label-free detection modalities for molecular sensing possess complimentary advantages and drawbacks. For instance, label based sensing systems are not susceptible to background effects as much as label-free systems. Susceptibility to background effects often limits the sensitivity of label-free systems. On the other hand, labeled systems such as fluorescence, which is the most common molecular detection modality in use today, suffer from low photon fluxes which limit their sensitivity, while label-free sensing systems (e.g., the Quadraspec biological compact disc system, such as described in the U.S. Pat. No. 6,685,885) have photon fluxes that are several orders of magnitude higher. 
         [0005]    Fluorescence label based systems suffer from additional problems such as photobleaching, which limits the ability to perform time-resolved studies beyond a certain length of time. Label-free systems generally do not suffer from such problems. 
         [0006]    Label based systems require an additional chemical processing step of attaching the “label” molecule to the molecule of interest. This process, in addition to increased processing time and cost, can alter the behavior of the molecules of interest. Label-free systems do not require this additional processing step. 
         [0007]    In spite of drawbacks such as the ones described above, fluorescent label based detection remains a widely used technology for molecular sensing applications, such as immunosensing and drug discovery, and possesses high sensitivity, especially in the detection of low molecular weight analytes and even single molecule detection. 
         [0008]    There are two main reasons for the observed performance of fluorescent label based systems compared to current label-free technologies. First, as mentioned earlier, fluorescent label based systems are not as susceptible to variations in background effects as label-free systems. Susceptibility to background effects can limit the sensitivity of label-free systems. Second, signal transduction in label-free systems is based on some physical property of the molecule of interest, which is often related to its molecular size. Coupled with the background problem, this molecular size dependency restricts the range of molecular size that can be detected reliably with label-free systems. For example, detection of low-molecular weights in immunoassay continues to be a challenge for many label-free systems and they try to get around the molecular size dependency through alternate assay formats such as reverse phase or inhibition assays. While the success of such approaches in circumventing the molecular weight dependency has been demonstrated, these approaches may not always be feasible. Label based systems on the other hand rely only on the properties of the “label” molecule and consequently work independent of the size of the molecule of interest. Thus they work equally well for large as well as small molecules and meet the demand for low molecular weight detection in many application areas. 
         [0009]    Even though fluorescent based systems have good performance compared to current label-free systems, the increasing demand for multiplexing is expected to put a significant strain on fluorescent based systems. This is because each molecule of interest requires a unique label. Although some approaches, such as Quantum Dots, have been proposed to address the “unique label” problem, considerable understanding of their interaction with bio-molecules will need to be built for them to emerge as a ubiquitous molecular sensing format. Label-free systems do not suffer from this limitation and as a result are attractive from the multiplexing point of view. 
         [0010]    From the items described above, it can be seen that the labeled and label-free molecular detection modalities can provide complimentary performance attributes. However, commercially available molecular sensing platforms do not exploit these complementary properties. Integrating these complementary molecular sensing modalities in a single platform can enhance the capabilities of either mode by providing capability to perform low molecular weight detection with high sensitivity as well as the ability of multiplexing without label limitations for suitable applications. 
         [0011]    With this objective in mind, exemplary embodiments of systems incorporating complementary molecular sensing modalities in a single platform are disclosed below. One embodiment integrates fluorescence based detection (most widely used label based detection) and interferometric based detection (most inherently sensitive label-free technology) into a single instrument. This instrument is capable of simultaneous data acquisition from both channels. The acquired data from both channels can be analyzed, and biologically relevant information, such as the amount of bound protein, can be extracted. 
     
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         [0012]      FIG. 1  shows a schematic of an embodiment of a data acquisition system; 
           [0013]      FIG. 2  is a flowchart for an instrument control program that can be used with the embodiment of  FIG. 1 ; 
           [0014]      FIG. 3A  shows an example of the results of the simultaneous acquisition of fluorescence and interferometric data; 
           [0015]      FIG. 3B  shows an example of the correlation between fluorescence and interferometric data from fluorescently labeled proteins immobilized on the surface of the biological compact disc; 
           [0016]      FIG. 4  illustrates an exemplary embodiment of an integrated fluorescence and interferometric microarray detection system; 
           [0017]      FIG. 5  shows specifications for a C5460-01 avalanche photodiode; 
           [0018]      FIG. 6  shows the spectral response and sampling frequency response for the -01 avalanche photodiode; 
           [0019]      FIG. 7  illustrates the noise character in fluorescence systems for different frequencies; 
           [0020]      FIG. 8A  shows the relationship between the fluorescence excitation efficiency and the reflection coefficient of the biological compact disc; 
           [0021]      FIG. 8B  shows the relationship between the sensitivity of in-line interferometric channel and the reflection coefficient of the biological compact disc; 
           [0022]      FIG. 8C  shows the relationship between the sensitivity of phase contrast interferometric channel and the reflection coefficient of the biological compact disc; 
           [0023]      FIG. 9A  shows an image of the fluorescence for a biological compact disk imaged simultaneously with both fluorescence and interferometric methods on the same protein grating pattern region shown in  FIG. 9B ; 
           [0024]      FIG. 9B  shows an image of the in-line interferometry for a biological compact disk imaged simultaneously with both fluorescence and interferometric methods on the same protein grating pattern region shown in  FIG. 9A ; 
           [0025]      FIG. 10A  shows the power spectrum corresponding to  FIG. 10A ; 
           [0026]      FIG. 10B  shows the power spectrum corresponding to  FIG. 10B ; 
           [0027]      FIG. 11A  shows the imaging from the interferometric channel at different phases in the experimental procedure in the upper four rows, and shows the imaging from the fluorescence channel in the bottom row; 
           [0028]      FIG. 11B  shows the response curve for the analyte concentration ladder on both the fluorescence and interferometric channels. 
           [0029]      FIG. 12A  illustrates protein molecules on the biological compact disk being illuminated with a focused Gaussian beam, polarization being indicated by the arrow; 
           [0030]      FIG. 12B  illustrates an angular coordinate system that can be used to calculate the angular distribution of intensity; 
           [0031]      FIG. 13A  illustrates that the reflection change is proportional to the thickness of the protein layer when the protein layer on the surface is thin enough (much less than the probe light wavelength); 
           [0032]      FIG. 13B  illustrates that if protein molecules agglomerate on the surface, then Mie scattering dominates and the scattering can be detectable in the Mie scattering channel; 
           [0033]      FIG. 14  illustrates schematically an embodiment of a four-channel microarray detection system that is capable of simultaneously acquiring four different signals from protein molecules on a biological compact disk, including fluorescence and Mie scattering channels (detected by a high-amplification APD), and amplitude and phase-contrast channels (interferometric channels, detected by a quadrant photodiode); 
           [0034]      FIG. 15  shows biological compact disk images with fluorescence and interferometric methods, the images were simultaneously captured with 4 channels: (A) Fluorescence; (B) Mie scattering; (C) Amplitude and (D) Phase contrast, on the same region of a protein grating pattern with a thickness of about 1˜4 nm (approx. a monolayer) that was illuminated at 488 nm; 
           [0035]      FIG. 16  shows the power spectra for the images shown in  FIG. 15 : (A) Fluorescence; (B) Mie scattering; (C) Amplitude and (D) Phase contrast channels; 
           [0036]      FIG. 17A  shows the spot intensities from the interferometry and fluorescence channels; 
           [0037]      FIG. 17B  shows the response curves for both the forward and reverse assays; 
           [0038]      FIG. 18A  shows the fluorescence channel for a two-channel acquisition of backfilled protein stripes at a concentration of 10 ug/ml collected simultaneously with the interferometry channel shown in  FIG. 18B ; 
           [0039]      FIG. 18B  shows the interferometry channel for a two-channel acquisition of backfilled protein stripes at a concentration of 10 ug/ml collected simultaneously with the fluorescence channel shown in  FIG. 18A ; 
           [0040]      FIG. 18C  shows the associated power spectra for the interferometry and fluorescence channel responses shown in  FIGS. 18A and 18B ; 
           [0041]      FIG. 18D  shows the correlation between the interferometry and fluorescence channel responses shown in  FIGS. 18A and 18B ; 
           [0042]      FIG. 19A  shows the fluorescence channel for a two-channel acquisition of backfilled protein stripes at a concentration of 10 ng/ml collected simultaneously with the interferometry channel shown in  FIG. 19B ; 
           [0043]      FIG. 19B  shows the interferometry channel for a two-channel acquisition of backfilled protein stripes at a concentration of 10 ng/ml collected simultaneously with the fluorescence channel shown in  FIG. 19A ; 
           [0044]      FIG. 19C  shows the associated power spectra for the interferometry and fluorescence channel responses shown in  FIGS. 19A and 19B ; 
           [0045]      FIG. 19D  shows the correlation between the interferometry and fluorescence channel responses shown in  FIGS. 19A and 19B ; 
           [0046]      FIG. 20A  shows the effects of bleaching on the fluorescence channel over time with the signal collected simultaneously with the interferometry channel shown in  FIG. 20B ; 
           [0047]      FIG. 20B  shows the lack of bleaching effects on the interferometry channel over time with the signal collected simultaneously with the fluorescence channel shown in  FIG. 20A ; 
           [0048]      FIG. 20C  is a graph of the average fluorescence and interferometry responses over time corresponding to the images shown in  FIGS. 20A and 20B ; 
           [0049]      FIG. 21   a  shows a portion of 6,800 spots printed on a region of a biological compact disc of which 3,400 are antibody spots and 3,400 are control spots, each antibody spot being adjacent to a control spot; 
           [0050]      FIGS. 21   b   1 - b   3  shows scans at different times in the experimental process by the interferometry channel in a simultaneous two-channel scan of interferometry and fluorescence channels:  FIG. 21   b   1  shows a scan of initial thickness,  FIG. 21   b   2  shows a scan after antigen binding; and  FIG. 21   b   3  shows a scan after secondary antibody binding; 
           [0051]      FIGS. 21   c   1 - c   3  shows scans at different times in the experimental process by the fluorescence channel in a simultaneous two-channel scan of interferometry and fluorescence channels:  FIG. 21   c   1  shows a scan of initial thickness,  FIG. 21   c   2  shows a scan after antigen binding; and  FIG. 21   c   3  shows a scan after secondary antibody binding; 
           [0052]      FIG. 22A  shows distributions of the height increment of antibody and control spots after antigen binding; 
           [0053]      FIG. 22B  shows distributions of the height increment of the antibody and control spots compared with the fluorescence signal of the antibody spots after secondary antibody binding; and 
           [0054]      FIG. 23  shows a scaling analysis of the fluorescence and interferometry channels. 
       
    
    
     DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS 
       [0055]    The embodiments of the present invention described below are not intended to be exhaustive or to limit the invention to the precise forms disclosed in the following detailed description. Rather, the embodiments are chosen and described so that others skilled in the art may appreciate and understand the principles and practices of the present invention. 
         [0056]    Fluorescence and interferometric signals have different angular distributions. Fluorescence excitation leads to isotropic (but not homogeneous) incoherent emission of radiation while the interferometric signal comes from coherently scattered radiation in the direction of the reflected light. This difference in angular distribution can be exploited in separating signals from the two channels in the instrument. 
         [0057]    Typically, fluorescence wavelength is longer than that of excited light due to energy loss of the excited molecules. The wavelength difference, called the Stokes&#39;s shift, provides another way to separate fluorescence from background light by using optical filters. 
         [0058]    An exemplary embodiment of a data collection system that collects both fluorescence and interferometric signals is shown schematically in  FIG. 1 . The system comprises a laser  10 , a linear stage (not shown), a spin motor (not shown) (e.g., Scanner motor from Laser Lines Ltd), a biological compact disc  12 , a photodetector  14 , an avalanche photodiode detector (“APD”)  16 , an analog-to-digital converter (“ADC”)  18 , a computer  19  and optical components such as mirrors, filters and lens. 
         [0059]    The biological compact-disc  12  is mounted on the spin motor capable of spinning at user defined speeds from 20 Hz to 100 Hz in increments of 20 Hz. The optical assembly is fixed to the linear stage which is capable of scanning with a resolution of 0.1 um. The combination of the spinning disc  12  and stage translation creates a polar coordinate system for referencing any point on the disc. Data from a given position of the linear stage constitutes a “track” on the disc  12 . Several such “tracks” are acquired with a user defined resolution, typically 20 microns, to build up the disc surface data in both acquisition channels. 
         [0060]    In the embodiment illustrated in  FIG. 1 , the illumination laser light from the laser  10  has a wavelength of 532 nm and serves as the probing light. The incoming laser beam is focused on to the disc using a lens L 3 , at oblique incidence. The reflected beam containing the interferometric signal is focused on to the photodetector  14  using another lens L 4 . Filters can be placed in front of the photodetector  14  to eliminate background radiation at wavelengths different from the incident laser wavelength. As mentioned earlier, fluorescence emission is isotropic. A fraction of fluorescence is collected using a high NA lens L 1  and is focused onto the APD  16  by a lens L 2 . Although, in principle, the fluorescence emission can be separated from the probe beam and direct reflection using differences in the angular distribution of fluorescence and interferometric signals, in practice, it is preferable to incorporate filters to eliminate stray scatter, such as from dust or sharp features on the disc, from making its way to the APD  16 . 
         [0061]    The signals from the APD  16  and the photodetector  14  are sent to a 2 channel ADC  18  for analog-to-digital conversion, after which they are sent to a computer  19 . Computerized data acquisition can be done using a system management program. A flowchart for an exemplary system management is shown in  FIG. 2 . 
         [0062]    At step  20 , the system devices and program are initialized for a data collection. At step  22 , the necessary scanning and data collection parameters are obtained and stored for use in the collection process. At step  24 , the system is moved to the starting position for data collection. At step  26 , the fluorescence signals from the APD  16  and the interferometric signals from the photodetector  14  are sent to the ADC  18  for analog-to-digital conversion, and, at step  29 , the converted signals are sent to the computer  19 . At step  30 , the stage is used to move the optical assembly to the next step for further data collection. At step  32 , the system determines whether the current position of the stage is less than or equal to the end position for data collection. If the current position is less than or equal to the end position, then control is transferred to step  34  which starts data collection at the next position and transfers control to step  26 . If the current position is greater than the end position, then control is transferred to step  36  which ends the collection program and shuts down the reader. 
         [0063]    The oblique incidence design incorporated in the instrument exploits the differences in the angular distribution of fluorescence and interferometric signals. The oblique design enables the spinning biological compact disc system to possess sufficient photon fluxes without using multiple filters for separation of the fluorescence emission from background light. 
         [0064]    Many, commercial fluorescence readers use Photo-Multiplier Tubes (PMTs) for detecting fluorescence emission. PMT&#39;s necessitate tight requirements on background shielding, protection from shock and so on. Alternatively, high-gain APDs such as the Hamamatsu C5460-01 can give comparable performance to PMTs but without the problems mentioned earlier. One important design consideration is the bandwidth of the APD which limits the acquisition speed. The high-gain APD  16  used in the embodiment of  FIG. 1  has a bandwidth of 100 kHz, which is sufficient to acquire data from a biological compact disc  12  spinning at 4800 rpm. 
         [0065]    Sufficient fluorescence emission efficiency is possible over a wide range of substrates. Therefore, the biological compact disc  12  is designed primarily based on the requirements for the label-free systems, which in this case is interferometric. Exemplary biological compact discs of the present embodiment include silicon discs coated with 100 nm of silica film. These discs are useful for commercial applications, particularly as they are inexpensive to manufacture yet still exhibit robustness and good sensitivity for all channels. Such discs are particularly useful for in-line interferometric channel sensitivity applications. 
         [0066]    For the embodiment illustrated in  FIG. 1 ,  FIG. 3A  shows an example of the readings from the simultaneous acquisition of fluorescence and interferometric data from an exemplary biological compact disc; and  FIG. 3B  shows an example of the quantitative correlation between the fluorescence and interferometric data. Such correlations can provide valuable information about the various biochemical processes involved in disc processing and molecular detection processes. For instance, in this example, fluorescently labeled antibodies are immobilized on the biological compact disc. The fluorescence channel quantifies the amount of the antibody while the interferometric channel quantifies the sum total of the interactions of all molecules present in the incubating solution, such as buffer, salts and other chemicals. In this case, the degree of correlation, or lack of correlation, between the two channels can tell us about the relative strength of the parasitic process such as binding of foreign molecules on the disc surface. Such information can help in optimizing disc processing steps by eliminating possible parasitic effects. This is a unique capability made possible by the integration of these complementary molecular detection modalities in a single platform. 
         [0067]    Another exemplary embodiment of a system for simultaneously acquiring fluorescence and interferometric signals on a substrate, such as a spinning microarray disk is shown in  FIG. 4 . Although fluorescence and interferometric signals both have scattering effects on probing light beams, their scattering properties have fundamental differences, such as their scattering distributions. With respect to interferometric signals, the scattering is mostly coherent (i.e., each molecule&#39;s scattering light is coherent with that of other molecules, and the total scattering light is coherent with incident and reflected light) and specular, in which Rayleigh scattering dominates. When illuminated with a coherent probe light, scattered light from the molecules superposes in the far field. The superposition induces the strongest intensity distribution of the scattering light along the reflected (specular) direction in the far field, and the scattered light interferes with the reflected light. As such, the signal of the target molecules is modulated in the reflected light. 
         [0068]    Fluorescence can be treated as incoherent scattered light within the dipole approximation. The incoherence is induced by the random relaxation time and phase of the fluorophore&#39;s excited energy level. As such, the fluorescence is incoherent, which means that without coherent superposition, the emitted fluorescence does not form a strong directional distribution, but rather emits into all solid angles. It should be noted that the distribution is also not homogenous and its distribution function can be determined without difficulty. Moreover, the unique spatial property of the fluorescence can help one to separate fluorescence and interferometric signals. 
         [0069]      FIG. 4  illustrates an exemplary embodiment of an integrated fluorescence and interferometric microarray detection system. The embodiment shown in  FIG. 4  comprises a laser  40  (e.g., INNOVA300 laser from Coherent Inc.), a linear stage  42  (e.g., MM2K stage from Newport), a spin motor  44  (e.g., Scanner motor from Laser Lines Ltd), a biological compact disk  46 , a quadrant detector  48  (e.g., PC50-6 from Pacific Silicon Sensor Inc.), an avalanche photodiode detector (“APD”)  50  (e.g., C5460-01 from Hamamatsu Company), an oscilloscope  52 , a computer  54  and some optical components such as mirrors, filters and lens. This embodiment is designed to acquire three channels simultaneously. The quadrant detector  48  is responsible for two interferometric channels, and the APD detector  50  acquires fluorescence signals from an analyte on the biological compact disk  46 . 
         [0070]    For mapping a whole disk, two free coordinates are established to form a polar coordinate system. The spinning motor  44  is used to rotate the biological compact disk  46  and serves as the angular coordinate when the motor spins in a selectable frequency ranging from about 20 Hz to about 80 Hz. The linear stage  42  serves as the polar coordinate and moves back and forth with 0.1 μm linear precision and 300 mm maximum travel distance. The motor  44  is fixed to the linear stage  42  so that two-dimensional mapping can be realized with appropriate computer control. This system is capable of mapping a 100 mm diameter biological compact disk in about 30 minutes with 2 μm by 2 μm pixel resolution. 
         [0071]    In this embodiment, the illumination from the laser  40  has a wavelength of about 488 nm and serves as the probing light. The laser beam is filtered, steered and focused onto the surface of the biological compact disk  46  with a filter, several mirrors and one 10 cm convex lens. The radius of the focal spot is about 20 μm on the disk  46 ; however, higher resolution can be achieved by switching to a 10 cm short focal length lens or even a microscope objective lens. The reflected light is guided into the quadrant detector  48 , which is responsible for acquiring the interferometric signals (i.e., phase contrast and in-line signals), and a 4 cm convex lens above the disk  46  gathers fluorescence and sends it into an APD  50  equipped with a 510 nm long-pass optical filter to block the scattered laser light. 
         [0072]    An oscilloscope  52  is responsible for acquiring the waveform for each scanned track of the disk  46 . The APD  50  and quadrant detector  48  are connected with three channels (e.g., channels  1 ,  2 ,  3 ) of the oscilloscope  52  via coaxial cables (see the lines from the oscilloscope to the detectors in  FIG. 1 ). Two of these cables are for the quadrant detector  48  so that it can acquire the two types of interferometric signals (i.e., phase contrast and in-line signals). Another coaxial cable connects the spin motor  44  to the oscilloscope  52 . The spin motor  44  generates a trigger signal for the oscilloscope  52 . The computer  54  controls the movement of the linear stage  42  and records data from the oscilloscope  52 . Two SCSI cables (see the lines from the computer in  FIG. 1 ) are used to connect the computer  54  to the linear stage  42  and to the oscilloscope  52 . 
         [0073]    The embodiment shown in  FIG. 4  has an oblique incidence design to benefit from the two distinct solid angular emission distributions caused by the different coherent properties of the fluorescence and interferometric signals. In an oblique incidence design, the probe laser beam is adapted to be incident obliquely and focus on the surface of the biological compact disk  46  to collect fluorescence with the convex lens above the disk. In this configuration, the reflected light does not enter the fluorescence collection lens, but the fluorescence can be acquired with good efficiency. Meanwhile, interferometric signals can be detected via acquiring the reflected probing light. In this way, two types of signals are detected simultaneously without influencing each other. 
         [0074]    As opposed to an oblique incidence design, traditional fluorescence detection systems collect fluorescence and reflected probing light together and then separate them with optical filters. While this method is practical for most common biosamples, when applied to a biological compact disk, the detection efficiency of the fluorescence can be low from the fluorophore monolayer (1˜10 nm thickness) on the surface. Empirically speaking, the photon flux ratio between the fluorescence and the probe light is about 1:10 7 . If the reflected probe light is mixed into the fluorescence channel, the extremely strong background light causes a large influence on the fluorescence detection precision. However, it has been found that if one or more long-pass filters are used, the background light can be minimized. In order to decrease the background light to a reasonable extent, 4 to 5 filters (as a filter stack) may be used in some embodiments. 
         [0075]    Since the photon flux of the fluorescence is low (about 1 nw for collection efficiency), the addition of the filter stack can negatively influence the low flux. More particularly, fluorescence flux is decreased by 25% for each filter used (i.e., when four filters are used, only 0.4% fluorescence survives). Moreover, the probe laser is not 100% pure. For instance, the INNOVA300 Argon laser generates mostly 488 nm wavelength light with 0.1 W operation power. However, there are still some long light wavelengths (e.g., 514 nm and 528 nm) with a ratio constituent above 0.01%. These wavelengths are inside the spectrum band of fluorescence so they are mostly immune to the 510 nm LP filter. As such, extra optical filters would be needed to purify the laser beam beforehand. 
         [0076]    Oblique incidence greatly minimizes the above-mentioned issues. More particularly, since reflected probe light does not affect fluorescence, only one filter is needed for wavelength filtering, and only one, or possibly even zero, optical filters are needed for laser purification. Thus, to achieve a low fluorescence flux, spatial filtering processes (such as the oblique incidence method) can help improve fluorescence collection efficiency and suppress background noise. 
         [0077]    High speed and sensitivity Avalanche photodiodes (APD) are widely used in low photon flux detection processes. In one exemplary embodiment of the present system, an APD (e.g., C5460-01 from Hamamatsu Photonics K.K.) serves as the fluorescence detector. As is seen in the exemplary datasheet of  FIG. 5 , the amplification of the APD is approximately 0.15 Gigavolt/W at 800 nm. Considering 520 nm as the central emission wavelength for fluorescein, it can be estimated that the real amplification for fluorescence, according to the spectral response curve, is 0.05 Gigavolt/W (see  FIG. 6 ). 
         [0078]    Background noise of the APD is expected to be 6 pW according to the noise equivalent power from the datasheet ( FIG. 5 ). Therefore, the detection limit of fluorescence is about 6 pW, without the aid of electronics (e.g., op-amp, frequency filters) or numerical signal enhancement approaches (e.g., signal processing such as FFT). According to tests of the present system, the detection limit is equivalent to 0.3 pm thickness of the protein layer conjugated with fluorescein, i.e. 0.3 pg/mm 2  protein planar density on the disk. 
         [0079]    Frequency response is another important parameter of the APD. This parameter sets the upper limit for the detection speed. As can be seen in  FIG. 5 , the signal frequency response is approximately 100 kHz, such that if the system scans 100 μm diameter protein spots on a biological compact disk with 0.05 second spin period (20 Hz), the central frequency for the spot signal can be estimated to equal 60 kHz (i.e., 20 Hz×0.3 m/0.1 mm) on the outer ring of disk. Therefore, a spin frequency of 20 Hz would be acceptable for a scanning system operating with a C5460-01 APD. If a higher spin frequency is demanded, then a lower amplification but higher response rate (such as C5460) could accommodate this requirement. 
         [0080]    As mentioned above, the fluorescence detection limit can be extended if the APD&#39;s noise is carefully analyzed and exploited, particularly since the frequency band of the fluorescence signal can be separated from the major band of the noise spectrum. 
         [0081]    Noise in fluorescence systems tends to be dominated by amplifier noise because of the associated low photon flux and high gain of these systems. This noise can have a 1/f character at low frequencies, and may have white noise properties at higher frequencies. The change in signal-to-noise with a change in the detection bandwidth depends on the frequency dependence. The different conditions are shown generically in  FIG. 7 . 
         [0082]    In the exemplary embodiment of the current invention, the laser beam passes rapidly over a succession of protein spots. Therefore, this embodiment constitutes a laser scanning configuration. Laser scanning can be accomplished either by a linear raster of the laser beam while the target remains fixed, or the laser beam can remain fixed while the target moves. In our case, the laser remains fixed and the target moves. The rotation of the spinning disc brings the same protein spot back to the probe laser many times. This represents high-speed sampling that has a strong advantage in the signal-to-noise ratio for scanning systems relative to static measurement systems. To show the advantages of high-speed spinning and scanning, we show how the signal-to-noise is improved over static measurements for the case of 1/f noise. 
         [0083]    Static Measurement with 1/f noise: For a static measurement, the signal from a target location is measured with an integration time T, after which the laser is moved (or the target is moved) to a new location to begin the next measurement. The effective sampling frequency in this case is f=1/T, and the effective bandwidth is BW=f=1/T. The noise in the signal is given by: 
         [0000]    
       
      
       P 
       N 
       =P 
       f 
       * BW/f=P 
       f  
      
     
         [0000]    and the detection bandwidth cancels the 1/f component of the noise, and no advantage is obtained by averaging. 
         [0084]    High-Speed Repetitive Measurements with 1/f noise: In this case, the sampling frequency is set by the transit time Δt from one spot on the disc to the next so f=1/Δt. The detection bandwidth is set by the integration time BW=1/T. The noise power is then given by 
         [0000]    
       
      
       P 
       N 
       =P 
       f 
       * BW/f=P 
       f 
       *Δt/T  
      
     
         [0000]    which is made smaller by choosing a shorter transit time (higher speed) and integrating longer. The comparison of the spinning detection noise to the static detection noise described above shows the clear advantages of high-speed spinning that are embodied in the biological compact disc concept. These noise arguments hold equally for both fluorescence and interferometry. The dual-mode detection we describe here therefore benefits directly from the high-speed spinning in the presence of 1/f noise. 
         [0085]    The following discussion about the electrical field of the disk is based on the condition that the incident light&#39;s polarization is parallel with the disk&#39;s surface. 
         [0086]    The surface of the biological compact disk is designed to enhance in-line and phase contrast sensitivities of the disk. This sensitivity can be predicted by determining the reflection coefficient r of the surface. Fluorescence sensitivity can also be determined by the reflection coefficient r. Because the analyte monolayer of the surface is thin (less than 10 nm, about 1/50 of the wavelength), the optical properties of the surface influence the fluorescence excitation efficiency, particularly since the surface electrical field is determined by the interference between the reflected light and the incident light. For example, when the reflection coefficient of the microarray surface is −1, the surface will be at the standing wave&#39;s node position. In this case, the electrical field is almost zero in the proximity of the surface so that the fluorophore will not be excited and the biolayer will not contribute a phase change. On the other hand, when the reflection coefficient of the microarray surface is +1, the electric field is a maximum in the proximity of the surface so that the fluorophore will be excited, and the biolayer contributes a maximum phase shift that would be detected in a phase-contrast detection system. 
         [0087]    A primary concept for the current embodiment of the invention is the optimum excitation of both fluorescence and phase-sensitive detection (either phase-contrast or in-line). In the case of r=+1, the maximum field automatically gives the maximum fluorescence and maximum phase contrast signal together. This is one exemplary embodiment of the current invention. 
         [0088]    In the case of in-line detection, there is a trade off between electric field strength at the surface and the condition of phase quadrature that must be set by the substrate structure. For in-line interferometry, the optimum phase condition is a pi/2 phase shift, but this phase condition produces half the electric field at the surface, which decreases both the phase contribution of the biolayer for interferometric detection and the fluorescence intensity. Therefore, a balance must be set in the design that keeps the surface field as large as possible, while also keeping a phase condition reasonably near to quadrature. 
         [0089]    Because the fluorescence excitation efficiency is proportional to the intensity of the electrical field, if the incident light&#39;s amplitude is E, then the surface electrical field is 
         [0000]      (1+r)E cos ωt 
         [0000]    on the disk surface, where r is the reflection coefficient. This relationship helps to predict the fluorescence excitation efficiency due to the optical property of the disk surface. As a result, the following conclusions can be reached: (1) if r=−1, the excitation efficiency is zero; (2) if r=1, the excitation efficiency is maximized; (3) if r=0, the excitation efficiency is half of the maximum value; and (4) the requirement for r is quite loose. In most situations, fluorescence excitation efficiency is rather large. This provides freedom to design a suitable reflection coefficient to accommodate the interferometric channel&#39;s sensitivity, since it is more rigorous for a suitable r. 
         [0090]    The three-dimensional plots of  FIG. 8  illustrate the relationship between r and the channel&#39;s sensitivity. Since r is a complex quantity, it needs two dimensions (modulus and phase) to be expressed.  FIG. 8A  shows the relationship between the fluorescence excitation efficiency and the reflection coefficient of the biological compact disc.  FIG. 8B  shows the relationship between the sensitivity of in-line interferometric channel and the reflection coefficient of the biological compact disc.  FIG. 8C  shows the relationship between the sensitivity of phase contrast interferometric channel and the reflection coefficient of the biological compact disc. 
         [0091]    Biological compact disks used in this embodiment can include silicon disks coated with 100 nm of silica film. These disks are useful for commercial applications, particularly because they are inexpensive to manufacture yet still exhibit robustness and good sensitivity for all channels. Such disks are particularly useful for in-line interferometric channel sensitivity applications. With respect to fluorescence detection applications, since fluorescence excitation efficiency is ∝|1+r| 2 , r can be calculated by considering the following factors: 
         [0000]                                                Incident angle   30 degrees           Polarization direction   parallel with disk&#39;s surface           index of air   1           index of silicon dioxide   1.46313           index of Silicon   4.379                        
It can be calculated that r=0.27−0.24i. Therefore, |1+r| 2 =1.67. This value is quite large considering that the maximum value is 2. In this case, the fluorescence excitation coefficient should be good, while the phase shift is close to the pi/2 phase required for in-line interferometric detection.
 
         [0092]    The present embodiment has been tested with gel-printed protein grating patterns and spot-style immunoassays. The former pattern can provide a periodic signal for system calibration and for the analysis of the signal power spectrum. The latter shows the system&#39;s potential applications for biological research. 
         [0093]    For the gel printed protein pattern, a physical adsorption method is used to immobilize protein molecules on the substrate surface. According to this example, a hydrophobic activation was performed on the silicon dioxide layer of the disk by surface silanization (the disks were soaked in 0.02M chlorooctadecylsilane Toluene solution for 12 hours). The proteins adhere to the silanized disk surface through hydrophobic interaction. Bovine serum albumin conjugated with fluorescein (A9771, Sigma corp.) is then printed on the disk in a grating pattern with a gel stamp method. The width of each protein stripe is about 100 um, and the gap between stripes is about 120 um. After printing, the surface of the disk is rinsed with de-ionized water and then blown dry with purified nitrogen to establish the protein layer as a monolayer. The results of two-channel scanning are shown in  FIG. 9 . On the same protein grating pattern region (whose thickness is about 1˜4 nm—approximately a monolayer), an imaging scan is performed simultaneously with two channels.  FIG. 9A  shows the light-scattering fluorescence, and  FIG. 9B  shows the in-line interferometry illuminated at 488 nm. The cross correlation value between  FIGS. 9A and 9B  is 0.83, thereby showing that the two results are highly correlated in this case. 
         [0094]      FIGS. 10A and 10B  show the power spectra that correspond to  FIGS. 9A and 9B , respectively, using the Fast Fourier Transform Method. The spikes on the spectrum shoulder come from the periodic protein stripe pattern. The Signal-to-Background Ratio (SBR) can then be derived from the spectrum chart. Here, since it is known that the thickness of the protein layer is about 1-3 nm (monolayer), the SBR for the fluorescence and interferometry channels are in the range of 300:1˜500:1. The detection limit for the lowest protein layer can be estimated as 1˜2.5 pm, i.e. 1˜2.5 pg/mm 2  planar density, which is close to the detection limit (i.e., 0.3 pg/mm 2 ), which is estimated from the APD detection limit as discussed above. 
         [0095]    It was also found that the first ‘spike’, which is the fundamental harmonic, is almost at the top of the spectrum shoulder, which exhibits the 1/f noise of the system (mostly originating from the APD). This indicates that target signal is not separated away from the 1/f noise frequency domain on this sample. This is because of the motor&#39;s low spinning frequency (20 Hz) and the relatively large distance between the protein stripes. When scanning smaller samples (e.g., sub-millimeter spots with 80 Hz spinning frequency), the SBR could be improved by about a factor of 10, which means that the detection limit can be extended to 0.1˜0.25 pg/mm 2 . 
         [0096]    This embodiment&#39;s capacity to quantify immunoassays with high background protein concentration was then tested. Only the fluorescence and amplitude channels were used because they have the highest SBR. In this exemplary illustration, the “sandwich model” immunoassay strategy is applied to a biological compact disk (i.e., 100 nm silica coated silicon disk). To detect the target antigen&#39;s concentration in the solution sample, which has a high background concentration, the corresponding antibody is immobilized on the disk, and then the disk is incubated with the analyte solution. Consequently, the antibody binds with the target antigen so that the antigen is anchored on the disk, while the background non-specific protein is washed off. When the target antigen is captured on the disk, the antigen can be incubated with a fluorescein-conjugated antibody (for fluorescence detection) or an unconjugated antibody (for interferometric detection). The fluorescence intensity or interferometric signal&#39;s increment is linearly related to the antigen concentration in the original solution. Using a standard responsive curve illustrating the relationship between the antigen concentration and the signal increment, it is possible to acquire the antigen concentration quantitatively. 
         [0097]    In an experimental procedure, eight wells of antibody spots are printed on an oxidized silicon disk. Each well includes a 2×2 array of spots arranged in a unit-cell configuration. The unit-cell configuration for this experiment comprises two spots on a first diagonal of anti-rabbit IgG, and two spots on the other diagonal of non-specific Horse IgG which are a control. These eight wells are incubated respectively with 0, 0.01, 0.03, 0.1, 0.3, 1, 3 and 10 ug/ml Rabbit IgG in 7 mg/ml rat lysate and then scanned. Thereafter, the spots are sequentially incubated with 20 ug/ml anti-rabbit-biotin, 20 ug/ml avidin, 20 ug/ml anti-avidin, with a scan being performed after each incubation process. 
         [0098]    The upper four rows of  FIG. 1A  show the thickness of the protein spots acquired from the interferometric channel. The first row shows the thickness of the spots after incubation with the series of rabbit IgG solutions in the concentration ladder. The second row shows the thickness of the spots after incubation with the anti-rabbit-biotin. The third row shows the thickness of the spots after incubation with the avidin. The fourth row shows the thickness of the spots after incubation with the anti-avidin-FITC. The fifth row shows fluorescence signals after incubation with anti-avidin-FITC. 
         [0099]      FIG. 1B  shows the response curves for the analyte concentration ladder on both the fluorescence and interferometric channels. In  FIG. 11B , the curves show spot thickness increments after each incubation process as a function of concentration. All of the curves are fitted with the Langmuir binding equation: 
         [0000]    
       
         
           
             
               Δ 
                
               
                   
               
                
               d 
             
             = 
             
               C 
                
               
                 
                   [ 
                   antibody 
                   ] 
                 
                 
                   
                     K 
                     D 
                   
                   + 
                   
                     [ 
                     antibody 
                     ] 
                   
                 
               
             
           
         
       
     
         [0000]    where K D  is the dissociation constant between antigen and antibody, or between avidin and biotin-conjugated protein. In the three curves for the interferometric channel, the increments increase monotonically with increasing concentrations indicating that the detection limit is below 10 ng/ml. The fluorescence response curve (upper solid curve) shows the same trend. As such, this experiment shows that the system succeeds in reaching 0.01 ug/ml detection limits on both the fluorescence and interferometric channels in the presence of 7 mg/ml complex protein background. 
         [0100]    Another exemplary embodiment comprises a four-channel detection method for protein-patterned biological compact disks that simultaneously measures fluorescence, Rayleigh scattering and/or diffraction, and two interferometric channels in orthogonal quadratures (i.e., a differential phase channel and a direct phase channel). The latter two channels constitute label-free interferometric protein detection, while fluorescence and Mie scattering detection provide complementary tools. 
         [0101]    Optical biosensors normally include a probe light and one or more detectors. When illuminated by probe light, protein molecules containing a fluorophore are excited and then emit fluorescence, or protein by itself scatters the probe light. By detecting fluorescence or scattered light, the protein information is obtained. For both cases, a discrete dipole approximation can be used to analyze the absorption, fluorescence, or scattering due to molecules. One sub-wavelength size molecule is considered as one discrete dipole when fluorescence or scattering occurs. Subsequently, a protein agglomerate or a protein layer on a surface could be treated as a group of dipoles. Within this approximation, the optical properties of the four channels are analyzed. 
         [0102]    Protein molecules are immobilized on the dielectric layers on the biological compact disk with complex reflection coefficient r. In the simplest model, molecules are distributed evenly (from a macroscopic view), and they are illuminated with a focused Gaussian laser beam whose waist diameter is D. The polarization is parallel with the surface, shown as the arrow parallel to the x-axis in  FIG. 12 . Other polarizations are also possible. Every molecule is a discrete dipole when illuminated with the probe light. 
         [0103]      FIG. 12A  illustrates protein molecules on a biological compact disk being illuminated with a focused Gaussian beam. Polarization is indicated by the arrow in  FIGS. 12A and 12B . Each molecule radiates fluorescence or scatters probe light in the manner of one discrete electric dipole.  FIG. 12B  illustrates a set of angular coordinates that can be used to calculate fluorescence, Rayleigh scattering (for interferometric channels) and Mie scattering angular distribution of intensity. 
         [0104]    A protein molecule has an inherent dipole moment {right arrow over (P)} even before excitation. The excitation probability of this dipole is proportional to sin 2  θ cos 2  φ (where θ and φ are angles of {right arrow over (P)} in the angular coordinates, shown in  FIG. 12B ). Within the mean lifetime (usually larger than 1 nanosecond) of the excited energy level, the dipole emits one photon. The probability of emission direction is proportional to sin 2  α (where α is the angle between the dipole moment and emission direction). To simplify this model, it can be assumed that the dipole moments are oriented isotropically in space. Because the relaxation time of excited molecules is random, and has at least one nanosecond variation, fluorescence from different molecules is incoherent. As a result, the fluorescence intensity distribution in the far field equals the algebraic sum of all the dipole intensities in the far field. 
         [0105]    Under these conditions, the fluorescence intensity angular distribution in the far field is: 
         [0000]    
       
         
           
             
               
                 
                   
                     F 
                      
                     
                       ( 
                       
                         θ 
                         , 
                         φ 
                       
                       ) 
                     
                   
                   = 
                     
                    
                   
                     
                       d 
                        
                       
                           
                       
                        
                       σ 
                     
                     
                       d 
                        
                       
                           
                       
                        
                       Ω 
                     
                   
                 
               
             
             
               
                 
                   = 
                     
                    
                   
                     K 
                      
                     
                       
                         ∫ 
                         
                           φ 
                           = 
                           0 
                         
                         
                           2 
                            
                           π 
                         
                       
                        
                       
                         
                           ∫ 
                           
                             
                               θ 
                               ′ 
                             
                             = 
                             0 
                           
                           π 
                         
                          
                         
                           
                             sin 
                             2 
                           
                            
                           
                             θ 
                             ′ 
                           
                            
                           
                             cos 
                             2 
                           
                            
                           
                             φsin 
                             2 
                           
                            
                           α 
                            
                           
                              
                             
                               Ω 
                               ′ 
                             
                           
                         
                       
                     
                   
                 
               
             
             
               
                 
                   = 
                     
                    
                   
                     K 
                      
                     
                       
                         ∫ 
                         
                           φ 
                           = 
                           0 
                         
                         
                           2 
                            
                           π 
                         
                       
                        
                       
                         
                           ∫ 
                           
                             
                               θ 
                               ′ 
                             
                             = 
                             0 
                           
                           π 
                         
                          
                         
                           
                             sin 
                             2 
                           
                            
                           
                             θ 
                             ′ 
                           
                            
                           
                             cos 
                             2 
                           
                            
                           
                             φ 
                              
                             
                               ( 
                               
                                 1 
                                 - 
                                 
                                   
                                     cos 
                                     2 
                                   
                                    
                                   α 
                                 
                               
                               ) 
                             
                           
                            
                           
                              
                             
                               Ω 
                               ′ 
                             
                           
                         
                       
                     
                   
                 
               
             
             
               
                 
                   = 
                     
                    
                   
                     K 
                      
                     
                       
                         ∫ 
                         
                           φ 
                           = 
                           0 
                         
                         
                           2 
                            
                           π 
                         
                       
                        
                       
                         
                           ∫ 
                           
                             
                               θ 
                               ′ 
                             
                             = 
                             0 
                           
                           π 
                         
                          
                         
                           
                             sin 
                             3 
                           
                            
                           
                             θ 
                             ′ 
                           
                            
                           
                             cos 
                             2 
                           
                            
                           
                             
                               φ 
                               ′ 
                             
                             ( 
                             
                               1 
                               - 
                               
                                 ( 
                                 
                                   
                                     sin 
                                      
                                     
                                         
                                     
                                      
                                     
                                       θcosφsinθ 
                                       ′ 
                                     
                                      
                                     cos 
                                      
                                     
                                         
                                     
                                      
                                     
                                       φ 
                                       ′ 
                                     
                                   
                                   + 
                                 
                               
                             
                           
                         
                       
                     
                   
                 
               
             
             
               
                 
                   
                     
                       
                           
                          
                         
                           
                             sin 
                              
                             
                                 
                             
                              
                             θsin 
                              
                             
                                 
                             
                              
                             
                               φsinθ 
                               ′ 
                             
                              
                             sin 
                              
                             
                                 
                             
                              
                             
                               φ 
                               ′ 
                             
                           
                           + 
                           
                             cos 
                              
                             
                                 
                             
                              
                             θcos 
                              
                             
                                 
                             
                              
                             
                               θ 
                               ′ 
                             
                           
                         
                         ) 
                       
                       2 
                     
                     ) 
                   
                    
                   
                      
                     
                       θ 
                       ′ 
                     
                   
                    
                   
                      
                     
                       φ 
                       ′ 
                     
                   
                 
               
             
             
               
                 
                   = 
                     
                    
                   
                     
                       
                         8 
                          
                         π 
                       
                       15 
                     
                      
                     
                       K 
                        
                       
                         ( 
                         
                           2 
                           - 
                           
                             
                               sin 
                               2 
                             
                              
                             
                               θcos 
                               2 
                             
                              
                             φ 
                           
                         
                         ) 
                       
                     
                   
                 
               
             
           
         
       
     
         [0000]    where K is a constant. From this equation, it is obvious that the fluorescence intensity reaches a maximum when 
         [0000]    
       
         
           
             
               φ 
               = 
               
                 
                   π 
                   2 
                 
                  
                 
                     
                 
                  
                 or 
                  
                 
                     
                 
                  
                 
                   
                     3 
                      
                     π 
                   
                   2 
                 
               
             
             , 
           
         
       
     
         [0000]    i.e. along the plane perpendicular to the polarization direction of the probe light.  1 his conclusion suggests the best fluorescence collection position. In the present system, the fluorescence collection lens is immediately above an illuminated region while the probe light is incident obliquely at 30 degrees. 
         [0106]    The reflection coefficient r of the biological compact disk surface also affects the fluorescence sensitivity. Because the protein layer on the surface is thin (less than 10 nm, about λ/50), the electromagnetic boundary condition of the surface imposes a large influence on fluorescence excitation efficiency. This is because the surface electric field is determined by interference between reflected and incidence light. For example, when the reflection coefficient r=−1 on the microarray surface, the surface will be at the nodal position of the resulting standing wave. In this case, the electric field is almost zero in the proximity of the surface so that the fluorophore will not be excited. 
         [0107]    Fluorescence excitation efficiency is proportional to the magnitude of the electric field. If the incident light amplitude is E, then the surface electric field is (1+r)E cos ωt on the disk surface, where the reflection coefficient r is a complex number. Therefore, the fluorescence excitation efficiency is proportional to |1+r| 2 . The fluorescence intensity angular distribution becomes: 
         [0000]      F(θ,φ)∝|1+r| 2 (2−sin 2  θ cos 2  φ) 
         [0000]    This equation is valid even after considering fluorescence reflected by the dielectric surface. 
         [0108]    Although both interferometric signals and fluorescence can be treated as dipole radiation from molecules, the optical properties have a fundamental difference and thus have different intensity distributions within the solid angle. Interferometric signals arise from coherent Rayleigh scattering. When illuminated with coherent probe light the dipole radiation superposes in the far field. The superposition causes the scattered light to be strongest in the reflected (specular) direction in the far field. For a thin protein layer, the superposed field calculated for dipole radiation coincides with the reflected light calculated using a thin film model. Therefore, to simplify computation the protein layer is treated as a dielectric thin film. 
         [0109]    Changes in the protein film changes the reflection coefficient of the biological compact disk. Interferometric channels detect the presence and thickness of the film by monitoring the reflection change. The change can be optimized by careful selection of r. The biological compact disk surface coating is designed to optimize the interferometric and fluorescence channel sensitivities. To optimize the response, the relationship between the reflection coefficient r of the biological compact disk and the reflection change due to a protein layer (see  FIG. 13A ) is determined.  FIG. 13A  illustrates that the reflection change is proportional to the thickness of the protein layer when the protein layer on the surface of the disk is thin enough (much less than the probe light wavelength). If the thickness of the protein layer is d, the refractive index is n p , and the reflection coefficient of the biological compact disk surface is r, then the protein layer on the biological compact disk has a new reflection coefficient r′ caused by the protein layer which is solved with the matrix method for calculating multiple dielectric layers to be: 
         [0000]    
       
         
           
             
               r 
               ′ 
             
             = 
             
               
                 
                   
                     ( 
                     
                       
                          
                         δ 
                       
                       - 
                       
                          
                         
                           - 
                           δ 
                         
                       
                     
                     ) 
                   
                    
                   
                     r 
                     0 
                   
                 
                 + 
                 
                   r 
                    
                   
                     ( 
                     
                       
                          
                         δ 
                       
                       - 
                       
                         
                           r 
                           0 
                           2 
                         
                          
                         
                            
                           δ 
                         
                       
                     
                     ) 
                   
                 
               
               
                 
                   ( 
                   
                     
                        
                       δ 
                     
                     - 
                     
                       
                         r 
                         0 
                         2 
                       
                        
                       
                          
                         
                           - 
                           δ 
                         
                       
                     
                   
                   ) 
                 
                 + 
                 
                   
                     r 
                      
                     
                       ( 
                       
                         
                            
                           
                             - 
                             δ 
                           
                         
                         - 
                         
                            
                           δ 
                         
                       
                       ) 
                     
                   
                    
                   
                     r 
                     0 
                   
                 
               
             
           
         
       
     
         [0000]    where r 0  is the reflection coefficient of the air-protein interface, and 
         [0000]    
       
         
           
             δ 
             = 
             
               
                 2 
                  
                 π 
                  
                 
                     
                 
                  
                 
                   n 
                   p 
                 
                  
                 d 
                  
                 
                     
                 
                  
                 cos 
                  
                 
                     
                 
                  
                 θ 
               
               λ 
             
           
         
       
     
         [0000]    is the phase change caused by the protein layer (single pass). Using this relationship along with the original reflection coefficient r, the new reflection coefficient r′, and the thickness of protein layer d, the presence and mass areal density of the protein molecule can be detected by monitoring the change of the reflection coefficient of the biological compact disk. There are two interferometric channels to monitor the reflection change. 
         [0110]    The amplitude channel directly detects the reflectance of the biological compact disk. It is called “amplitude channel” because this channel detects the intensity of the reflected radiation that interferes with the light scattered by the protein molecules. Because of the condition of phase quadrature that is established when the reflection coefficient has a pi/2 phase shift, or nearly so, the phase associated with the protein layer is transduced into intensity (amplitude) at the detector. When the system is scanning a protein layer, the reflectance change is: 
         [0000]      Δ I   R   =I   0 (| r′|   2   −|r|   2 ) 
         [0000]    If the thickness of the protein layer is thin (much less than the probe light wavelength), ΔI R  is approximately proportional to the protein layer thickness. With knowledge of r and the reflectance change, the thickness of the protein layer is calculated. 
         [0111]    The phase-contrast channel detects the differential phase change of the reflection coefficient. When the system scans the edge of the protein layer, part of the focused spot is reflected with r while the other part is reflected with r′. In the far field, the reflected direction will slightly depart from the original direction, and the shifted angle is proportional to the phase difference between r and r′. A quadrant photodetector (position-sensitive detector) is used to detect this angle shift. The detector sensing window is divided into four quadrants. The center of the reflected light falls evenly on the center so that all quadrants have the same signal. When the reflection angle shifts, the photon flux on the quadrants acquire a small difference. The relation between this difference and the thickness of the protein layer is: 
         [0000]        ΔI   φ   =TI   0 (φ′−φ+2δ tan θ p /tan θ 0   51  r| 2    
         [0000]    where φ′ and φ are the phase of r′ and r, θ 0  is the incident angle, θ p  is the refraction angle in the protein layer, and T is the coefficient which converts phase shift into center shift signal ΔI φ . Simulations calculate T to be approximately 0.5 in this embodiment. 
         [0112]      FIG. 13B  illustrates that if protein molecules agglomerate on the surface, Mie scattering dominates, and the scattering can be detectable in the Mie scattering channel. In this embodiment, the Mie scattering channel shares the same optical path with the fluorescence channel, but it could have a separate lens and detector, or share the same lens and use a beamsplitter to direct the scattering channel to a separate detector. Usually, Rayleigh scattering is centered along the reflection direction because of the interference and the redistribution of the scattered electric field. But for larger agglomerations of protein molecules, if the agglomeration size is comparable or even larger than the wavelength of the probe light, then scattered light is detectable away from the reflection direction (see  FIG. 13B ). This provides an opportunity to separate a scattered signal from light reflected by the dielectric surface to eliminate the background. With appropriate filters, the system can switch between fluorescence and Mie scattering channels, or with the beamsplitter the two channels could be acquired simultaneously with separate detectors. The potential of the Mie scattering channel can be further exploited because protein agglomeration is a common phenomenon on a microarray surface. When the particles are large, even Mie scattering can be predominantly in the forward direction. Therefore, in one embodiment, the Mie channel photodetector could be situated on either side of the intrferometric channel. It is also possible to use different quadrants of a quadrant detector to detect the Mie scattering and the interferometric channels separately. In this embodiment, the lower quadrants could be summed or differenced to obtain the in-line and phase-contrast signals, respectively, while the upper quadrant could be used to detect the low-angle forward-scattered Mie scattering. 
         [0113]    In the current embodiment, experiments were performed with a biological compact disk having a multilayer dielectric stack structure of ten repeated layers of SiO 2  and Ta 2 0 5  with thicknesses of 113.4 nm and 72.2 nm, respectively, on a glass substrate. Working under the condition of a 30° obliquely incident s-polarized 488 nm laser beam, the surface reflection coefficient is r=−0.58−0.35i. The fluorescence and interferometric channels were appropriately optimized for this biological compact disk. 
         [0114]    An oblique incidence design was established for this system to benefit from two distinct solid angular emission distributions due to the different coherent properties of fluorescence and interferometric signals. In oblique incidence, the probe laser beam is incident obliquely on the biological compact disk, and fluorescence is collected with a convex lens above the disk. In this configuration, the reflected light does not enter the fluorescence collection lens, but fluorescence can be acquired with high efficiency. Interferometric signals are detected by acquiring the reflected probe light. In this way, two types of signals are detected simultaneously without influencing each other. The reason for this design is that the fluorescence efficiency is very low from the fluorophore-conjugated protein layer (1˜10 nm thickness) on the surface. Empirically, the ratio of photon flux between fluorescence and probe light is about 1:10 7 . If reflected probe light is mixed into the fluorescence channel, the extremely strong background causes a large influence on the fluorescence detection precision. Long-pass filters alone may not be enough to eliminate the background. Spatial filtering, as from oblique incidence, improves the fluorescence collection efficiency and suppresses background. 
         [0115]    One embodiment of a four-channel microarray detection system is shown schematically in  FIG. 14 . This system is capable of simultaneously acquiring four different signals from protein molecules on a biological compact disk. These four channels are: fluorescence and Mie scattering channel (detected by a high-amplification APD  90 ), amplitude and phase contrast channel (interferometric channels, detected by a quadrant photodiode  88 ). The embodiment illustrated in  FIG. 14  comprises a laser  80  (Innova300, Coherent Inc.), a linear stage  82  (MM2K, Newport), a spinning motor  84  (Scanner motor, Lincoln Laser, Inc.), a biological compact disk  86 , a quadrant detector  88  (PC50-6, Pacific Silicon Sensor Inc.), an APD  90  (C5460-01, Hamamatsu Company), an oscilloscope  92 , a computer  94  and optical components such as mirrors, filters and lenses. The system is now discussed with a focus on the following three categories: light path, scanning mechanism, and electronics. 
         [0116]    To map the entire disk, the scanning mechanism uses a polar coordinate system. The spin motor  84 , on which the biological compact disk  86  is mounted, provides the angular coordinates when the motor  84  spins in a selectable frequency ranging from 20 Hz to 80 Hz. A linear stage  82  provides the radial coordinate. In the experimental embodiment, the linear stage  82  can move back and forth with 0.1 um linear precision and 300 mm maximum travel distance. The spin motor  84  is fixed on the linear stage  82  so that two-dimensional mapping can be realized with appropriate control by the computer  94 . This system is capable of mapping a 100 mm diameter of the biological compact disk in 30 minutes with 2 um by 2 um pixel resolution. 
         [0117]    The illumination laser light emitted by the laser  80  has a wavelength of 488 nm. The laser beam is steered and focused onto the surface of the biological compact disk  86  with a filter, several mirrors and one 10 cm convex lens. The radius of the focal spot is about 20 um on the disk  86 . Higher resolution can be achieved by switching the 10 cm lens with a short focal-length lens or a microscope objective lens. The reflected light is guided into the quadrant detector  88  which is responsible for acquiring the interferometric signals (amplitude and phase contrast channels). A 4 cm convex lens above the biological compact disk  86  gathers fluorescence or Mie scattering radiation and sends it to the APD  90 . A 510 nm long-pass optical filter  96  effectively blocks the scattered laser light for fluorescence detection. The long-pass optical filter  96  is removed from the optical path for detection of the Mie scattering signal with this channel. 
         [0118]    The oscilloscope  92  acquires waveforms for each scan track. The APD  90  and the quadrant detector  88  are input into three channels of the oscilloscope  92  by coaxial cables. Two cables are connected to the quadrant detector  88  to acquire the two types of interferometric signals (i.e., amplitude and phase contrast). One cable is connected to the APD  90  to sequentially acquire the fluorescence signal and the Mie scattering signal depending on whether the long pass filter  96  is in the optical path. One more coaxial cable connects the stage  82  to the oscilloscope  92  for the stage  82  to send a trigger signal to the oscilloscope  92 . The computer  94  controls the linear stage  82  and records data from the channels of the oscilloscope  92 . 
         [0119]    This system has been tested with Gel-printed protein grating patterns and spotted patterns of antibodies. The former provide a periodic signal for system calibration and signal power spectrum analysis. The latter shows the system detection for immunological assays. 
         [0120]    In the gel-printed protein patterns, the protein molecules are immobilized by physical adsorption following hydrophobic activation of the silicon dioxide surface of the disk by silanization (disks soak in 0.02M chlorooctadecylsilane toluene solution for 12 hours). Proteins bind with the silanized disk surface through hydrophobic interaction. Bovine serum albumin (BSA) conjugated with fluorescein (A9771, Sigma Corp.) is printed on the disk in a grating pattern with a gel stamp method. Each protein stripe width is 100 um, and the gap between two stripes is 120 um. After printing, the disk surface is rinsed with deionized water then blown dry with purified nitrogen. Because the protein is conjugated with fluorescein (absorption wavelength of 492 nm), the four-channel system is able to image the protein pattern in both the fluorescence and the interferometric channels. 
         [0121]      FIG. 15  shows the signals collected from the four channels with this biological compact disk. On the same region of the protein grating pattern, whose thickness is about 1˜4 nm (approx. a monolayer), imaging is simultaneously performed with the four channels.  FIG. 15A  shows the fluorescence signal captured by the APD  90 .  FIG. 15B  shows the Mie scattering signal captured by the APD  90 .  FIG. 15C  shows the amplitude signal captured by the quadrant detector  88 .  FIG. 15D  shows the phase contrast signal captured by the quadrant detector  88 . 
         [0122]    The data in  FIGS. 15A ,  15 C, and  15 D show strong signals from the patterned protein, while the Mie scattering data in  FIG. 15B  is virtually blank. This means that protein molecules are printed evenly and did not agglomerate. However in other experiments, strong Mie scattering has been observed in this channel. Upon observing the Mie scattering data more carefully, a “stain” was found near the top-right corner which could be due to a dust particle or agglomerated protein. The cross-correlation value is 0.83 between the fluorescence channel in  FIG. 15A  and the amplitude interferometry channel in  FIG. 15C , demonstrating that the fluorescence and amplitude channels are highly correlated, although not identical, with the differences caused by differences between specific and nonspecific mass binding, and also caused by differences in fluorophore microenvironments on the disc. 
         [0123]      FIGS. 16A-D  show the power spectra corresponding to the data in  FIGS. 15A-D , respectively. The power spectra for fluorescence is shown in  FIG. 16A ; the power spectrum for Mie scattering is shown in  FIG. 16B ; the power spectrum for the amplitude interferometric channel is shown in  FIG. 16C , and the power spectrum for the phase contrast interferometric channel is shown in  FIG. 16D . The family of peaks in the spectra comes from the periodic protein stripe pattern. The signal-to-background ratio (SBR) for the power spectra in  FIGS. 16A ,  16 B,  16 C and  16 D are respectively: 532:1, 1:1, 617:1, and 98:1. The amplitude channel and the fluorescence have similar SBR values, indicating that the sensitivities are almost equal in these cases. The phase-contrast channel SBR is relatively low but still considered strong. The thickness of the protein layer is 1˜3 nm in this experiment. The detection limit for the lowest detectable protein density is estimated to be 2˜6 pm, or about 2˜6 pg/mm 2  areal density. 
         [0124]    In the power spectra graphs of  FIG. 16 , the first-order signal frequency is almost at the top of the spectrum shoulder, which arises from the 1/f noise of the system combined with surface roughness of the disc. This indicates that the target signal may not be separated from the 1/f noise frequency domain in this experiment. This is because of the low spin frequency of the motor  84 , about 20 Hz, and the relatively large distance between the protein stripes. By scanning on smaller protein patterns, such as submilimeter spots, with 80 Hz spinning frequency the SBR can be improved by more than a factor of 10 which extends the detection sensitivity to 0.2˜0.6 pg/mm 2 . 
         [0125]    It is important to note that 1/f noise is not equivalent to surface roughness. Noise is stochastic and changes from circuit to circuit of the disc. In contrast, surface roughness is a fixed property of the disc and can be measured with the high accuracy of the interferometric metrology. Therefore, this surface roughness is not noise, but can be measured accurately and subtracted accurately between a pre- and a post-scan that seeks to measure the amount of bound protein. It is when the surface is measured accurately and subtracted that the sensitivity of this technique achieves low values such as 0.2 to 0.6 pg/mm 2 . 
         [0126]    This embodiment of an integrated protein microarray detection system, can perform fluorescence, interferometry and Mie scattering simultaneously on a protein-patterned biological compact disk. Biological compact disk structures optimized for each channel were fabricated and tested with periodic protein patterns. The results show that both interferometric and fluorescence channels can achieve a 5 pg/mm 2  detection limit. The immunoassay experiment showed the four-channel system potential for immunoassays with high-concentration backgrounds. The system detected 10 ng/ml target protein in 7 mg/ml lysate. 
         [0127]    In another embodiment we explore the difference between a forward and a reverse assay. Fluorescence compared to interferometry shows important differences in this comparison. This experiment is shown in  FIG. 17 . The unit cells in this case have anti-goat antibody printed on one diagonal to bind antigen from sample, while the opposite diagonal has printed rabbit antigen to capture antibody from sample. The sample consists of FITC-conjugated anti-rabbit cultured in goat. In a single incubation both a forward and a reverse assay can be evaluated in both the interferometric and the fluorescence channels on the two opposite diagonals. The incubations were made with increasing sample concentrations of 0, 0.03, 0.1, 0.3, 1, 3, 10, and 30 ug/ml. The spot intensities from the interferometry and fluorescence channels are shown in  FIG. 17A . The response curves for both the forward and reverse assays are shown in  FIG. 17B . It is clear from the response curves that the reverse assay has a much stronger response than the forward assay. This general trend is captured by both the interferometric and fluorescence channels. However, there are quantitative differences between interferometry and fluorescence that can highlight different mechanisms between forward and reverse assays. 
         [0128]    To provide further calibration and correspondence between interferometry and fluorescence, a two-channel acquisition of backfilled protein stripes at a concentration of 10 ug/ml is shown in  FIG. 18 . The fluorescence channel is shown in  FIG. 18A , and the interferometry channel is shown in  FIG. 18B , with the associated power spectra in  FIG. 18C . The correlation between the two channels is shown in  FIG. 18D . There is clean separation between the bright and the dark stripes with strong correlation in the corresponding values. These data show strong cross-validation of the interferometry and fluorescence channels. 
         [0129]    To test the detection limits, stripes were backfilled at a concentration of 10 ng/ml. The results are shown in  FIG. 19 .  FIG. 19A  shows the fluorescence channel,  FIG. 19B  showa the interferometric channel,  FIG. 19C  shows the corresponding power spectra, and  FIG. 19D  shows the correlation. There is still separation between the positive and negative stripes in the correlation. This concentration is near the detection limit for this approach that uses gel printing. Inhomogeneities in the gel printing technique limit the sensitivity. 
         [0130]    A key difference between interferometry and fluorescence is the quenching phenomenon that is associated with fluorescence but not with interferometry. One of the drawbacks of fluorescence is the destruction of the fluorophore, called bleaching, during illumination. To illustrate the power of the present multi-mode detection system, the bleaching of fluorescence was measured simultaneously in both an interferometric and a fluorescence channel. The results are shown in  FIG. 20 .  FIG. 20A  shows the fluorescence channel and  FIG. 20B  shows the interferometry channel. In this experiment the radius of the probe beam was not changed. The same track was measured repeatedly. During the scan, the fluorophore slowly quenched, seen in  FIG. 20A  with time increasing downward. However, in the interferometry channel seen in  FIG. 20B  there is no bleaching. This is seen in the graph in  FIG. 20C . The interferometry channel is flat with time, while the fluorescence is bleached. This serves to illustrate fundamental differences between interferometry and fluorescence that the current invention exploits. 
         [0131]    An extensive demonstration of dual fluorescence and in-line interferometry is shown  FIG. 21 . In this example the disc was printed with 25,000 protein spots. Half were anti-rabbit and the other half were control spots. The disc was incubated with rabbit in a forward-phase assay, then followed with the sandwich that had a fluorescent tag. This demonstrates the differences between forward and sandwich assays in a micro-spot format. It also shows the use and comparison of the fluorescence channel to the interferometry channel. The second row of  FIG. 21  is the interferometry channel, and the bottom row is the fluorescence channel. The fluorescence only appears in the final sandwich incubation. 
         [0132]    On the disc, there were 3,400 antibody spots (anti-rabbit IgG, R2004, Sigma Company) and 3,400 control spots (anti-mouse IgG, R2004, Sigma Company) printed on one region of the biological compact disc (one disc can hold 50,000 spots). Each antibody spot is adjacent to one control spot. The spot diameter was 200 μm.  FIG. 21   a  shows one part of the 6,800 spots. A two-channel scan (scan 1) was performed to record the initial thickness and fluorescence of these spots (see  FIGS. 21   b   1  and c 1 , a small area of the microarray is shown for better viewing). The biological compact disc was incubated with 10 ng/ml rabbit IgG (I5006, Sigma Company) in PBST (PBS+0.05% Tween). Bovine serum at 100 μg/ml (B8655, Sigma Company) is spiked in the solution as background protein. A two-channel scan (scan 2) measured the interferometric and fluorescent signal change due to the antigen binding (see  FIGS. 21   b    2  and c 2 ). A secondary antibody formed sandwich assay to evaluate the two-channel detection limit. The biological compact disc is further incubated with 1 μg/ml anti-rabbit-FITC (F9887, Sigma Company) in PBST. A third scan (scan 3) measured the two-channel response due to the secondary antibody binding (see  FIGS. 21   b   3  and c 3 ). 
         [0133]    In the analysis, the interferometric channel tracks the specific binding between anti-rabbit IgG and rabbit IgG.  FIG. 22A  shows the height increment of the antibody spots and control spots after incubation with 10 ng/ml rabbit IgG solution. In a histogram of the height increments of all spots, the centers of the specific and control Gaussian distributions are separated by a difference of 0.097 nm. The standard deviations of the two distributions are respectively 0.10 nm and 0.106 nm. So the standard errors are 0.10/√{square root over (3400)}=0.0017 nm and 0.0018 nm. If the antibody spot thickness increment is linear to antigen level at low concentration, the detection limit of interferometric channel is estimated as 250 pg/ml for the forward-phase assay. The fluorescence channel detects no signal at this stage because the antigen has no bound fluorophore. 
         [0134]      FIG. 22B  shows the height increment of the antibody and control spots compared with the fluorescence signal of the antibody spots after incubation with the anti-rabbit-FITC. The detection limit of the interferometric channel is estimated as 71 pg/ml. The detection limit is lower than forward-phase assay because one antigen can bind with several antibodies in the sandwich assay. The detection limit of the fluorescence channel is estimated as 31 pg/ml. 
         [0135]    From the statistical analysis in  FIG. 23 , the scaling capabilities of both the fluorescence and interferometry channels can be further demonstrated by studying sub-populations of spots on the disc. Scaling is important for microarrays because it shows the potential for expanding the numbers of assay on a disc for highly multiplexed assays. The change in the standard error as the population size changes provides information about spatial correlations on the disc. The scaling analysis is shown in  FIG. 23 . The scaling varies nearly as the square root of the number of elements in the populations. This indicates that spatial correlations are mostly absent on the disc. The similar scaling between the fluorescence and interferometric channels provides important cross-validation of these two channels. 
         [0136]    While exemplary embodiments incorporating the principles of the present invention have been disclosed hereinabove, the present invention is not limited to the disclosed embodiments. Instead, this application is intended to cover any variations, uses, or adaptations of the invention using its general principles. Further, this application is intended to cover such departures from the present disclosure as come within known or customary practice in the art to which this invention pertains.