Patent Publication Number: US-7221632-B2

Title: Optical disc system and related detecting methods for analysis of microscopic structures

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application is a continuation-in-part of U.S. application Ser. No. 10/043,688 filed Jan. 10, 2002, which is a continuation-in-part of U.S. application Ser. No. 10/008,156 filed Nov. 9, 2001 now U.S. Pat. No. 7,061,594. 
     This application also claims the benefit of priority from U.S. Provisional Applications 60/305,043 filed the Jul. 12, 2001, 60/307,487 filed Jul. 24, 2001, and 60/322,863 filed Sep. 12, 2001. These applications are herein incorporated by reference in their entireties. 
    
    
     BACKGROUND OF THE INVENTION 
     1. Field of the Invention 
     The present invention relates generally to optical discs and optical disc readers. In particular, the invention relates to the use of standard optical disc drives, and slightly modified drives, to permit discriminable acquisition of a variety of different types of signals from an optical disc. The optical discs in such use include optical bio-discs having encoded information as well as investigational structures or features that are deposited on external or internal surfaces of the disc. 
     2. Description of Related Art 
     Commonly assigned, co-pending U.S. patent application Ser. Nos. 09/183,842 and 09/311,329 describe methods and apparatus for detecting operational and investigational structures on one or more surfaces of an optical disc assembly. Some of the methods and apparatus discussed in these applications detect investigational structures by physically modifying certain processing circuits in the optical disc drives. As an alternative to these and similar approaches, the present invention is directed to utilizing a principal advantage of relying on standard optical disc readers for laser microscopic detection. This advantage includes the ubiquitous distribution of such drives in the current consumer environment. Therefore, it would be desirable to provide methods and apparatus for detecting operational and investigational structures on an optical disc assembly without having to physically modify the processing circuitry herein. 
     To provide some background for further discussion of the present invention, relevant features of a conventional optical disc reader and optical disc are described briefly in connection with  FIGS. 1–7 . For purposes of preliminary introduction these figures will be briefly described.  FIG. 1  is a cross-sectional view of typical single-layer CD or CD-like disc and a schematic representation of a reader associated therewith.  FIG. 2  is a side cross-sectional view of the disc shown in  FIG. 1  at greater magnification.  FIG. 3  is a perspective view of the surface of a CD-R disc with wobble grooves.  FIG. 4  is a schematic representation of an optical disc detector and associated electronics that use three beams for tracking, focusing, and reading.  FIG. 5  is a plan view that illustrates the position of beams from a typical three-beam pickup relative to a track on an optical disc.  FIG. 6  is a block diagram of a known optical disc reader. And,  FIG. 7  is a functional block diagram of a conventional digital signal processing circuit. 
     More particularly now,  FIG. 1  depicts the reader&#39;s optical pickup or objective assembly  10  and a conventional CD-type optical disc  11  with a light path indicated as dashed lines. For clarity,  FIG. 1  depicts a minimal complement of the optical pickup components.  FIG. 2  provides a side cross-sectional enlarged view of disc  11  in the same orientation relative to the incident light. 
     With reference to  FIGS. 1 and 2 , the conventional optical pickup  10  includes light source  19 , lenses  12 ,  13 , and  14 , beam splitter  15 , quarter wave plate  20 , and detector  18 . Light source  19  is placed at a focal point of a collimator lens  12  that normally has a long focal distance. Collimator lens  12  makes the divergent light rays parallel. A monitor diode (not shown) may be used to stabilize the laser&#39;s output. Light source  19  may be a laser, LED, or laser diode, although the present invention may be implemented on a non-coherent light system as well. 
     A conventional optical design used for three-beam pickup typically uses two secondary beams for tracking. To generate these beams, light from source  19  passes through diffraction grating  17 , which is a screen with slits spaced only a few laser wavelengths apart. As the beam passes through the grating, the light diffracts; when the resulting collection is again focused, it will appear as a single, bright, centered beam with a series of successively less intense beams on either side. It is this diffraction pattern that actually strikes the disc. 
     A conventional three-beam pickup uses the center beam for reading data and focusing and two secondary beams for tracking only. In this design, the beams are spatially linked because they are the result of a single diffracted laser beam. By contrast, a one-beam pickup accomplishes all of these tasks using a single beam. 
     Polarization beam splitter  15  (PBS) directs the light to a disc surface and then directs the reflected light to the photodiode sensor  18 . PBS  15  normally includes two prisms with a common 45° face acting as a polarizing prism. Collimator lens  12  preferably follows PBS  15 . The light then passes through the quarter-wavelength plate  20 , which is an anisotropic material that rotates the plane of polarization of the light beams. Light that has passed through quarter-wavelength plate  20  and that has been reflected from disc  11  back again through quarter-wavelength plate  20  will be polarized in a plane at right angles to that of the incident light. Because PBS  15  passes light in one plane, (e.g., horizontally polarized) but reflects light in the other plane (e.g., vertically polarized), PBS  15  deflects the reflected beam toward sensor  18  to read the digital data. 
     The final piece of optics in the optical path to disc  11  is objective lens  13 , which is used to focus the beams onto the disc data surface, taking into account the refractive index of the light-proximal polycarbonate substrate  112  of disc  11 . Objective lens  13  focuses the light into a convergent cone of light, or light spot. The convergence is a function of the numerical aperture of the lens. 
     The data encoded on disc  11  now determines the fate of the laser light. In a regular CD, when the light spot strikes a land, the smooth interval between two pits, light is almost totally reflected. When it strikes a pit with a depth of about a quarter wavelength of the light, diffraction and cancellation due to interference cause less light to be reflected. All three intensity-modulated light beams return through objective lens  13 , quarter-wavelength plate  20 , collimator  12 , and PBS  15 . Finally, these beams pass through singlet lens  14  and an astigmatic element  16 , which may be a cylindrical lens, to introduce astigmatism in the reflected light beam en route to photodiode  18 . 
     As shown in greater detail in  FIG. 2 , CD-type disc  11  includes three layers from the light-proximal surface to the light-distal surface. By convention, disc layers are numbered upwards from the light-proximal surface to the light-distal surface. These layers include the transparent substrate  112 , a reflective layer  114 , and a protective layer  116 . Transparent substrate  112  makes up most of the thickness of a typical CD-type disc, as measured along the optical axis, and provides both optical and structural features necessary for disc operation. 
     Transparent substrate  112  is typically impressed or embossed with a spiral track that starts at the innermost readable portion of the disc and then spirals out to the outermost readable portion of the disc. In a non-recordable disc (e.g., pre-recorded), this track is made up of a series of embossed pits, each typically having a depth of approximately one-quarter the wavelength of the light that is used to read the disc. The pits have varying lengths. The length and spacing of the pits is employed as the mechanism for encoding the data. 
     With reference now to  FIG. 3 , the spiral groove in a recordable disc contains a dye rather than pits. A typical recordable disc includes a spiral groove having a characteristic shape along the length thereof. This type of groove is known as a “wobble groove,” and is formed by a bottom portion having undulating or wavy sidewalls. A raised or elevated portion separates adjacent grooves in the spiral. Such a wobble groove may then include embossed portion  110  and groove portion  118  as shown in  FIG. 3 . Embossed portion  110  and groove portion  118  are similar to the wobble groove found on a standard recordable CD. 
     Referring now to  FIG. 4 , the exemplary detector  18  and its associated electronics are described in more detail. Detector  18  typically includes a central detector  25 , and can be bordered by additional side detector elements  26  and  27 . Central detector  25  may be split into multiple detector elements (e.g., four), represented as A, B, C, and D. Detector elements A, B, C, and D (sometimes collectively referred to as a “quad detector”) each provide an electrical signal indicative of the intensity of the reflected light beam striking that element. 
     The sum of the signals from the quad detector  25 , e.g., A+B+C+D, provides a radio frequency (RF) signal  50 , also referred to as a high frequency (HF), quad-sum, or sum signal. As used herein the notation “A+B” indicates the sum of the signals from detector elements A and B. The HF signal  50  (i.e., RF, quad-sum, or sum signal) is typically demodulated to recover data recorded on the optical disc. 
     Various pairs of the signals from detector elements A to F are also combined to provide feedback signals for tracking and focus control. For example, a tracking signal  52  (e.g., tracking error or TE signal) is obtained from the difference between the E and F signals, (i.e., E−F). A focus error (FE) signal  54  may be obtained from the difference between the A+C and B+D signals. 
     Typically, such processing is performed by analog circuitry in combination with one or more integrated circuit chips. Often, the circuitry takes the form of a special chip set or a single ASIC (application-specific integrated circuit) chip. 
     The circuitry of  FIG. 4  is just one example of circuitry that provides focus and tracking error signals in an optical disc player. Numerous methods are known for providing these signals. For example, a focus error signal may be obtained by the critical angle method, described in U.S. Pat. No. 5,629,514 or the Foucault and astigmatism methods, described in  The Compact Disc Handbook  by Pohlmann, A-R Editions, Inc. (1992) both of which are incorporated herein by reference in their entireties. Similarly, tracking error signals may be obtained using the single beam push-pull or three beam methods described in  The Compact Disc Handbook  or the differential phase method described in U.S. Pat. No. 5,130,963, which is incorporated herein by reference in its entirety, or the single beam high frequency wobble method. 
     With reference now to  FIG. 5 , a CD drive typically uses a three-beam pickup, in which the light beam is split into three beams, a main beam  21  and two tracking beams  23 . The main beam  21  is focused onto the surface of an optical disc so that it is centered on a tracking structure, whereas the tracking beams  23  fall on opposite sides of the tracking structure. Main beam  21  is shown centered on track  24  (as defined by pits  22 ), with tracking beams  23  falling on opposite sides of track  24 . By design, the three beams are reflected from the optical disc and directed to detector  18  ( FIG. 4 ) so that main beam  21  falls on the quad detector, and tracking beams  23  fall on sensor elements E and F. 
       FIG. 6  is a generalized block diagram of an illustrative chip set  30  for a typical optical drive system. Although the chip sets for CD, CD-R, and DVD drives can be somewhat different from one another, it will be understood that the system shown in  FIG. 6  is meant to generically represent all types of optical drives, and that a detailed understanding of the differences between the chip sets is not necessary to practice the present invention. 
     The HF signal  50 , obtained from summing the signals from detector elements A, B, C, and D, is normally processed to extract whatever data is recorded on the optical disc. First, analog HF signal  50  is conditioned, with normalization and equalization performed. Next, analog signal  50  is converted to a digitized signal including a serial stream of digital data referred to as channel bits. The channel bit stream is then demodulated according to the modulation standard used for the type of optical disc being read. For example, it is common for CD-type discs to use eight-to-fourteen (also denominated “eight-of-fourteen”) modulation (EFM) wherein a data byte, or eight data bits, is encoded into fourteen channel bits. There are three merging bits between each group of fourteen channel bits. Thus, when reading a CD-type optical disc, seventeen channel bits are read from the optical disc, the merging bits are discarded, and the remaining fourteen bits are decoded, or demodulated, to obtain the original data byte. The data bytes themselves are grouped into blocks, which are further processed to reduce the effects of disc defects, such as scratches on the disc surface. 
     HF signal  50  from detector  18  ( FIG. 4 ) may be converted to a square wave signal  51  by comparator  31 , which provides a high output when HF signal  50  is above a threshold level, and a low output when HF signal  50  is below the threshold. Digital signal processing circuit (DSP)  32  then samples the resulting square wave signal  51  to determine the value of each channel bit. DSP  32  further demodulates the channel bits to extract the data bytes that are then grouped into blocks and processed to correct errors that may have occurred. Memory  33   a  provides temporary storage for the data, as it is being processed by DSP  32  and assembled into blocks. 
     Servo block  34  analyzes the tracking error (TE) signal  52  (or a wobble tracking error (WTE) in a DVD or CD-R system) and provides a tracking control signal to the tracking mechanisms to ensure that the pickup assembly maintains proper tracking. Similarly, a focus control signal  53  is provided based on focus error (FE) signal  54 . DSP  32  provides an indication of the data rate of HF signal  50 , which is used by servo block  34  to provide a speed control signal  55  to the spindle motor (not shown) of the optical disc drive. 
     In an audio CD player, after processing by DSP  32 , each data block is sent to audio reproduction circuitry not shown in  FIG. 6 . However, in some data storage applications, each data block may contain additional error detection codes (EDC) and error correction codes (ECC). EDC/ECC circuitry  35  typically uses the EDC and ECC codes to increase the integrity of the data block by detecting and correcting errors not already corrected by DSP  32 . Memory  33   b,  which may be combined with memory  33   a,  provides temporary storage for data blocks being processed by EDC/ECC circuitry  35 . Finally, the data blocks are transferred from the optical disc player to host  37  by means of interface circuitry  36 . Although an ATAPI interface is shown, it will be understood that other interfaces, such as SCSI, Firewire, or Universal Serial Bus (USB) and the like could also be used. 
     A controller  38  coordinates the operation of the various components of chip set  30 , for example, by coordinating the transfer of data blocks between DSP  32  and EDC/ECC circuitry  35 . Controller  38  also keeps track of which data block is being read and may keep track of various parameters indicative of the operational status of the optical disc reader. 
     Program memory  39  contains program code for the operation of controller  38 . In many optical disc reader chip sets, program memory  39  may also contain program instructions for DSP  32  or EDC/ECC circuitry  35 . This is advantageous for manufacturers in that the operation of the disc drive may be changed by altering the program code in program memory  39 . For example, a newly developed method of modulating or encoding data on an optical disc may be accommodated by changing program memory  39 . 
       FIG. 7  is a functional block diagram illustrating the signal processing that occurs within DSP chip  32  when configured in a conventional manner. As shown, DSP  32  performs several functions. For example, DSP  32  typically normalizes and/or equalizes the HF signal (block  40 ); converts the normalized HF signal from the analog-to-digital (block  42 ); demodulates and decodes the resulting EFM signal (block  44 ); performs some type of error checking procedure (e.g., using Cross-Interleaved Reed-Solomon Code “CIRC” block  46 ); and provides the resulting signal to an output interface (block  48 ) for communication with the host data bus  37  ( FIG. 6 ). Examples of commonly used DSP chips that perform some or all of these functions include the SAA 7210, SAA 7220, and the SAA 7735, available from Philips Electronics Corporation, Eindhoven, Netherlands. 
     While the foregoing description is sufficient for a basic understanding of the present invention, there are numerous alternative designs and configurations of an optical pickup and associated electronics, which may be used in the context of the present invention. Further details and alternative designs are described in  Compact Disc Technology,  by Nakajima and Ogawa, IOS Press, Inc. (1992);  The Compact Disc Handbook, Digital Audio and Compact Disc Technology,  by Baert et al. (eds.), Books Britain (1995);  CD - Rom Professional&#39;s CD - Recordable Handbook: The Complete Guide to Practical Desktop CD,  Starrett et al. (eds.), ISBN:0910965188 (1996); all of which are incorporated herein in their entirety by this reference. 
     SUMMARY OF THE INVENTION 
     It is an object of the present invention to overcome limitations in the known art. It is a further object of the present invention to adapt a known optical disc system to read an optical disc assembly and extract both operational information used to operate the optical disc system and indicia data indicative of a presence of an investigational feature associated with the optical disc assembly. 
     These and other objects and advantages of the present invention are achieved in an optical disc system that includes a photo detector circuit of an optical disc drive and a signal processing system. The photo detector circuit of the optical disc drive is configured to generate at least one information-carrying signal from an optical disc assembly. The signal processing system is coupled to the photo detector circuit to obtain from the at least one information-carrying signal both operational information used to operate the optical disc system, and indicia or characteristic data indicative of a presence of an investigational feature associated with the optical disc assembly. 
     The present invention is also directed to a method that includes depositing a test sample, spinning the optical disc assembly, directing an incident beam, detecting a return beam, and processing the detected return beam to acquire information about an investigational feature associated with the test sample. The step of depositing a test sample positions the sample at a predetermined location on an optical disc assembly. The step of spinning the optical disc assembly is directed to spinning the disc assembly in an optical disc drive. The step of directing an incident beam directs the beam onto the optical disc assembly. The step of detecting a return beam detects the returned beam formed as a result of the incident beam interacting with the test sample. 
     Other advantages of the present invention are achieved in an alternative method that includes acquiring a plurality of analog signals, summing a first subset of the plurality of analog signals, combining a second subset of the plurality of analog signals, obtaining information used to operate an optical disc drive, and converting the sum signal to a digitized signal. The step of acquiring a plurality of analog signals includes receiving return light from the optical disc assembly using a plurality of photo detectors. The step of summing a first subset of the plurality of analog signals produces a sum signal. The step of combining a second subset of the plurality of analog signals produces a tracking error signal. The step of obtaining information used to operate the optical disc drive includes processing the tracking error signal. 
     An alternative method of the present invention includes adapting a portion of a signal processing system, acquiring a plurality on analog signals, converting the analog signals into a digitized signal, and characterizing investigational features on an optical disc assembly based on the digitized signal. The step of adapting a portion of a signal processing system adapts the system to operate as an analog-to-digital converter. The step of acquiring a plurality on analog signals acquires the signals from a photo detector circuit of an optical disc drive. The plurality of analog signals include information that is indicative of the investigational features. The step of converting the analog signals into a digitized signal converts the signals using the signal processing system. 
     A specific implementation of this method includes steps of receiving and converting. The step of receiving includes receiving at least one analog signal at a corresponding input of signal processing circuitry. The at least one analog signal is provided by at least one corresponding photo detector element that detects light returned from a surface of the optical disc assembly. The step of converting includes converting each of the at least one analog signal into a corresponding digitized signal. Each digitized signal is substantially proportional to an intensity of the returned light detected by a corresponding one of the at least one photo detector elements. 
     More specifically, the present invention is directed to an optical disc system including a photo detector circuit of an optical disc drive configured to generate at least one information-carrying signal from an optical disc assembly. The optical disc system is further provided with a signal processing system coupled to the photo detector circuit to obtain from the at least one information-carrying signal both operational information used to operate the optical disc system and indicia data indicative of a presence of an investigational feature associated with the optical disc assembly. 
     In one embodiment, the signal processing system includes a PC and analog-to-digital converter coupled between the at least one information carrying signal and the PC. The analog-to-digital converter may advantageously provide a digitized signal and the PC may include a first program module to detect and characterize peaks in the digitized signal. In this embodiment, the PC may further include a second program module to detect and count double peaks in the digitized signal. In addition, the signal processing system may also further include an analyzer coupled between the analog-to-digital converter and the PC. In this embodiment, the analog-to-digital converter provides a digitized signal, and the analyzer includes logic to detect and characterize peaks in the digitized signal. According to one aspect of this embodiment, the analyzer further includes logic to detect and count double peaks in the digitized signal. 
     Alternatively, the optical disc system may include a signal processing system that has an audio processing module coupled between the at least one information-carrying signal and the analog-to-digital converter. In this alternate implementation, the optical disc system further includes a predetermined sound recorded on the optical disc assembly, and a program module in the PC for detecting the indicia data in a deviation of the at least one information carrying signal from the predetermined sound when the investigational feature is present. The predetermined sound may be encoded silence. 
     In another embodiment, the signal processing system further includes a buffer coupled between the at least one information-carrying signal and the analog-to-digital converter. The signal processing system may further advantageously include a trigger detection circuit coupled to the analog-to-digital converter, the trigger detection circuit being operative to detect a particular time in relation to a time when the indicia data is present in the at least one information-carrying signal. 
     In yet another implementation of the present invention, the signal processing system includes a programmable digital signal processor selectively configurable to extract the operational information from the at least one information-carrying signal while in a first configuration and operate as an analog-to-digital converter to provide the indicia data while in a second configuration. According to an aspect of this implementation of the invention, the signal processing system may include a PC, a programmable digital signal processor coupled to the at least one information-carrying signal, and an analyzer coupled between the programmable digital signal processor and the PC so that the analyzer provides the indicia data. 
     In many of the specific implementations and embodiments of the present invention, the signal processing system may advantageously be provided with a trigger detection circuit that detects a time period during which the investigational feature associated with the optical disc assembly is scanned by the photo detector circuit, or alternatively a trigger detection circuit that detects a particular trigger time in relation to a respective time duration during which the indicia data is present in the at least one information-carrying signal, and each respective time duration occurs periodically with a respective investigational feature and a corresponding set of indicia data. 
     According to one aspect of the audio implementation of this invention, the signal processing system includes a PC and an audio processing module coupled between the PC and the at least one information-carrying signal. The audio processing module may be selected one of either an external module independent of the optical disc drive, a drive module that is a part of the optical disc drive, or a modified drive module that is a part of the optical disc drive. The PC may advantageously include a processor coupled to the audio module, and a software module stored in a memory to control the processor to extract the indicia data from audio data. 
     In one principal embodiment of the present invention, the photo detector circuit includes circuitry to generate an analog signal as the at least one information-carrying signal. The analog signal including one of a high frequency signal from a photo detector, a tracking error signal, a focus error signal, an automatic gain control setting, a push-pull tracking signal, a CD tracking signal, a CDR tracking signal, a focus signal, a differential phase detector signal, a laser power monitor signal, and a sound signal. 
     According to other aspects of this invention, the optical disc system may include an optical disc assembly having disposed thereon the associated investigational feature in a first disc sector and encoded thereon the operational information used to operate the optical disc drive in a remaining disc sector. The optical disc assembly may include a reflective-type or transmissive-type optical disc. The optical disc assembly may include a trigger mark disposed thereon in a predetermined position relative to the first disc sector. In this embodiment, the signal processing system includes a trigger detection circuit that detects the trigger mark. 
     In accordance with certain aspects hereof, the trigger detection circuit detects the trigger mark periodically. The trigger detection circuit may detects the trigger mark either at (i) a predetermined time in advance of, (ii) a time at, or (iii) a predetermined time after a time when a respective investigational feature is read by the photo detector circuit based on the predetermined position of the trigger mark relative to the first disc sector. 
     In alternative designs of one principal embodiment of the optical disc system, one or more additional photo detector circuits are configured to generate at least one information-carrying signal from a respective optical disc assembly. The optical disc assembly may include one or more reporters having an affinity for a respective investigational feature. One or more of the reporters may be individually selected from the group consisting of plastic micro-spheres, colloidal gold beads, silica beads, glass beads, latex beads, polystyrene beads, magnetic beads, and fluorescent beads. 
     According to another aspect of the present invention, there is provided an assay method which includes the steps of (1) depositing a test sample at a predetermined location on an optical disc assembly, (2) spinning the optical disc assembly in an optical disc drive, (3) directing an incident beam onto the optical disc assembly, (4) detecting a return beam formed as a result of the incident beam interacting with the test sample, and (5) processing the detected return beam to acquire information about an investigational feature associated with the test sample. In this method the optical disc assembly may include one or more reporters having an affinity for investigational features in the test sample. These reporters may be individually selected from the group consisting of plastic micro-spheres, colloidal gold beads, silica beads, glass beads, latex beads, polystyrene beads, magnetic beads, and fluorescent beads. 
     In this embodiment of the present method, the step of detecting a return beam may form a plurality of analog signals. The step of processing the detected return beam may advantageously include (1) summing a first subset of the plurality of analog signals to produce a sum signal (2) combining one of the first subset and a second subset of the plurality of analog signals to produce a tracking error signal, (3) obtaining information used to operate an optical disc drive from the tracking error signal, and (4) converting the sum signal to a digitized signal. This method may optionally include the additional step of detecting a trigger mark associated with the optical disc assembly. 
     Another assay method according to certain aspects of this invention includes the steps of (1) depositing a test sample at a predetermined location on an optical disc assembly (2) spinning the optical disc assembly in an optical disc drive, (3) directing an incident beam onto the optical disc assembly, (4) detecting a transmitted beam formed as a result of the incident beam interacting with the test sample and continuing through the disc assembly, and (5) processing the detected transmitted beam to acquire information about an investigational feature associated with the test sample. This method may include the further steps of detecting a reflected beam formed as a result of the incident beam interacting with the test sample, and processing the detected reflected beam to acquire information about an investigational feature associated with the test sample. This method may also include the optical disc assembly having one or more reporters with an affinity for investigational features in the test sample. As with the prior method discussed above, in this method the one or more reporters may be individually selected from the group consisting of plastic micro-spheres, colloidal gold beads, silica beads, glass beads, latex beads, polystyrene beads, magnetic beads, and fluorescent beads. 
     Also in this method, the step of detecting a transmitted beam forms a plurality of analog signals. Similarly, the step of processing the transmitted beam may include the additional steps of (1) summing a first subset of the plurality of analog signals to produce a sum signal, (2) combining one of the first subset and a second subset of the plurality of analog signals to produce a tracking error signal, (3) obtaining information used to operate an optical disc drive from the tracking error signal, and (4) converting the sum signal to a digitized signal. This method may optionally include the additional step of detecting a trigger mark associated with the optical disc assembly. 
     Yet another method of this invention includes the steps of (1) acquiring a plurality of analog signals from an optical disc assembly using one or more photo detectors, (2) summing a first subset of the plurality of analog signals to produce a sum signal, (3) combining a second subset of the plurality of analog signals to produce a tracking error signal, (4) obtaining information used to operate an optical disc drive from the tracking error signal, and (5) converting the sum signal to a digitized signal. In this alternative method, the steps of acquiring and summing produce the sum signal, and the sum signal includes perturbations indicative of an investigational feature positioned at a location on the optical disc assembly. This method may include the further step of characterizing the investigational feature based on the digitized signal. 
     In this method, the step of converting may include configuring a portion of an optical disc drive chip set to operate as an analog-to-digital converter. In one embodiment, this configuring step includes programming a digital signal processing chip within the optical disc drive chip set to operate as an analog-to-digital converter. The digital signal processing chip may advantageously be provided with a normalization function, an analog-to-digital converter function, a demodulation/decode function, and an output interface function. In this specific embodiment, the step of configuring may further include by-passing the sum signal around the demodulation/decode function by creating a path from the analog-to-digital converter function to the output interface function. And, the step of configuring may also include deactivating the demodulation/decode function. 
     According to one principal aspect of this method, the step of converting includes configuring a digital signal processing chip that includes a normalization function, an analog-to-digital converter function, a demodulation/decode function, and an output interface function. And, the step of configuring includes creating a path from the analog-to-digital converter function to the output interface function so that the sum signal is unprocessed by the demodulation/decode function. Herein, the step of configuring may similarly include deactivating the demodulation/decode function. 
     In accordance with one aspect of this method, the step of acquiring may include tapping one or more of the plurality of analog signals directly at the one or more photo detectors. And, the step of converting may include directing the signals into an analog-to-digital converter. In a particular embodiment, the step of converting further includes directing the analog signals from the one or more photo detectors into a buffer amplifier before processing by the analog-to-digital converter. 
     Alternatively, the step of acquiring may include tapping one or more of the plurality of analog signals after processing by an optical disc drive chip set, while the step of converting may then include directing the signals into an analog-to-digital converter. In this alternative embodiment, the step of converting may similarly include directing the analog signals from the optical disc drive chip set into a buffer amplifier before directing the analog signals into the analog-to-digital converter. 
     According to still another aspect of this invention, there is provided an alternative method including the steps of (1) adapting a portion of a signal processing system to operate as an analog-to-digital converter (2) acquiring a plurality of analog signals from a photo detector circuit of an optical disc drive, the plurality of analog signals including information therein that is indicative of investigational features on an optical disc assembly (3) converting the analog signals into a digitized signal with the signal processing system, and (4) characterizing the investigational features based on the digitized signal. In this embodiment, the step of adapting may include programming a digital signal processing chip within the signal processing system to operate as the analog-to-digital converter. 
     Still yet a further method according to this invention includes the steps of (1) receiving each of at least one analog signal at a corresponding input of signal processing circuitry, the at least one analog signal having been provided by at least one corresponding photo detector element that detects light returned from a surface of an optical disc assembly, and (2) converting each of the at least one analog signal into a corresponding digitized signal, each digitized signal being substantially proportional to an intensity of the returned light detected by a corresponding one of the at least one photo detector element. In this method, the step of converting may advantageously include operating the signal processing circuitry to bypass any demodulation of a first digitized signal. In this embodiment, the step of converting may further include the steps of (1) operating the signal processing circuitry to bypass any decoding of the first digitized signal, and (2) operating the signal processing circuitry to bypass any checking for errors in the first digitized signal. 
     Alternatively, the step of converting may include operating the signal processing circuitry to bypass any decoding of a first digitized signal. As an alternative thereto, the converting step may include operating the signal processing circuitry to bypass any checking for errors in a first digitized signal. 
     The different embodiments of this method may each include the further step of combining at least two of the at least one analog signal when there are two or more such signals. In this embodiment, the step of combining is a step selected from a group consisting of adding, subtracting, dividing, and multiplying, and any combination thereof. The step of combining may be performed before, or alternatively after, the step of converting. 
     The method of claim  55  wherein the step of receiving includes at least one analog signal provided by at least one corresponding photo detector element that detects light transmitted through an optical disc assembly. 
     Generally for this method, the step of receiving may include detection of a trigger mark indicative of a time period during which the investigational feature associated with the optical disc assembly is scanned by the at least one photo detector. Also any of these embodiments may further include a step of supplying a first digitized signal of the at least one digitized signal at an output interface of the signal processing circuitry after the step of converting without substantially modifying the first digitized signal between the steps of converting and supplying. In these embodiments, the signal processing circuitry includes a digital signal processor or, alternatively, an external analog-to-digital converter. In the A/D converter implementation, the signal processing circuitry may further include a buffer amplifier before the external analog-to-digital converter. 
     According to other aspects of this invention, the characteristic signals generated hereby are considered inventive in their own right. Thus the present invention is further directed to a signal characteristic of information about an investigational feature located in an optical disc assembly, the signal being generated by a process including the steps of (1) depositing a test sample at a predetermined location on an optical disc assembly, (2) spinning the optical disc assembly in an optical disc drive, (3) directing an incident beam onto the optical disc assembly, (4) detecting a return beam formed as a result of the incident beam interacting with the test sample, and (5) processing the detected return beam to acquire information about an investigational feature associated with the test sample. The return beam may be formed as a result of the incident beam interacting with one or more reporters having an affinity for investigational features in the test sample. The step of detecting the return beam may form a plurality of analog signals. In this embodiment, the step of processing the detected return beam may include (1) summing a first subset of the plurality of analog signals to produce a sum signal, (2) combining one of the first subset and a second subset of the plurality of analog signals to produce a tracking error signal, (3) obtaining information used to operate an optical disc drive from the tracking error signal, and (4) converting the sum signal to a digitized signal. The signal may then include distinctive perturbations indicative of an investigational feature located at a location of the optical disc assembly. As above, the step of converting may include configuring a portion of an optical disc drive chip set to operate as an analog-to-digital converter. And, the step of configuring may include programming a digital signal processing chip within the optical disc drive chip set to operate as an analog-to-digital converter. 
     In one specific embodiment of the process employed to generate the desired signal, the digital signal processing chip includes a normalization function, an analog-to-digital converter function, a demodulation/decode function, and an output interface function. In this embodiment, the step of configuring may further comprises passing the sum signal around the demodulation/decode function by creating a path from the analog-to-digital converter function to the output interface function. Also, the step of configuring may further include deactivating the demodulation/decode function. 
     In another specific embodiment of the process employed to generate the desired signature signals, the step of converting may include directing the sum signal into an external analog-to-digital converter. In this embodiment, the step of converting may further include directing the sum signal into a buffer amplifier prior to the external analog-to-digital converter. 
     In yet a further specific embodiment of the process employed to generate the desired signal signatures, the step of converting may include configuring a digital signal processing chip that includes a normalization function, an analog-to-digital converter function, a demodulation/decode function, and an output interface function, while the step of configuring includes creating a path from the analog-to-digital converter function to the output interface function so that the sum signal is unprocessed by the demodulation/decode function. 
     In many of these signal generating processes, the step of detecting may further include detecting a transmitted beam formed as a result of the incident beam interacting with the test sample and passing through the optical disc assembly. 
     Additionally, the step of detecting the return beam may form a plurality of analog signals and the step of processing the detected return beam may include (1) summing a first subset of the plurality of analog signals to produce a sum signal, (2) combining a second subset of the plurality of analog signals to produce a tracking error signal, (3) obtaining information used to operate an optical disc drive from the tracking error signal, and (4) converting the sum signal to a digitized signal. In these embodiments, the sum signal advantageously includes perturbations indicative of an investigational feature located at a location of the optical disc assembly. 
     The step of converting may include configuring a portion of an optical disc drive chip set to operate as an analog-to-digital converter. In these embodiments, the step of configuring may include programming a digital signal processing chip within the optical disc drive chip set to operate as an analog-to-digital converter. In a more specific implementation thereof, the digital signal processing chip includes a normalization function, an analog-to-digital converter function, a demodulation/decode function, and an output interface function. In these specific embodiments, the step of configuring may further include passing the sum signal around the demodulation/decode function by creating a path from the analog-to-digital converter function to the output interface function. Also, the step of configuring may further include deactivating the demodulation/decode function. 
     In certain embodiments of the process for generation the desired signal signatures, the step of converting includes configuring a digital signal processing chip that includes a normalization function, an analog-to-digital converter function, a demodulation/decode function, and an output interface function, while the step of configuring comprises creating a path from the analog-to-digital converter function to the output interface function so that the sum signal is unprocessed by the demodulation/decode function. 
     The unique signal signatures of the present invention may also be generated by a process including the steps of (1) adapting a portion of a signal processing system to operate as an analog-to-digital converter, (2) acquiring a plurality of analog signals from a photo detector circuit of an optical disc drive, wherein the plurality of analog signals includes information therein that is indicative of investigational features on an optical disc assembly, (3) converting the analog signals into a digitized signal with the signal processing system, and (4) characterizing the investigational features based on the digitized signal. In this process, the step of adapting may include programming a digital signal processing chip within the signal processing system to operate as the analog-to-digital converter. Also, the step of acquiring may include tapping the analog signals prior to an optical drive buffer. And, the step of acquiring may include trigger mark signals indicative of a time period during which the investigational feature associated with the optical disc assembly is scanned by the photo detector circuit. 
     According to still other aspects of this invention, there is provided a method of detecting a signal within an optical disc system, which method includes the steps of (1) generating an incident beam of known wavelength, (2) directing the beam onto an optical disc containing an investigational feature, and (3) receiving a return beam formed as a result of the incident beam interacting with the investigational feature. In this method the optical disc may comprise one or more reporters having an affinity for the investigational feature, the reporters being capable of interacting with the incident beam. One or more of the reporters may be individually selected from the group consisting of plastic micro-spheres, colloidal gold beads, silica beads, glass beads, latex beads, polystyrene beads, magnetic beads, and fluorescent beads. Also in this method, the step of receiving may further include receiving a transmitted beam formed as a result of the incident beam interacting with the investigational feature, and passing through the optical disc. Generally, the step of receiving may advantageously involve use of one or more photo detectors. The step of receiving may form a plurality of analog signals for processing by a signal processing system. In addition, the signal processing system may include an external analog-to-digital converter and with or without a buffer amplifier associated therewith. In the embodiment utilizing the buffer amplifies, the analog signals may be tapped prior to processing by an internal optical disc drive buffer circuit. In certain implementations of these aspects of the present invention, the signal processing system may include programmable digital signal processing circuitry or audio processing circuitry. 
     According to yet still additional aspects of the present invention, there is provided a method of imaging an investigational feature including the steps of (1) depositing an investigational feature at a predetermined location on an optical disc assembly, (2) spinning the optical disc assembly in an optical disc drive, (3) directing an incident beam onto the optical disc assembly, (4) detecting a return beam formed as a result of the incident beam interacting with the investigational feature, (5) processing the detected return beam to acquire information about an investigational feature, and (6) imaging the investigational feature based on the information. In this method, the optical disc assembly may be provided with one or more reporters having an affinity for investigational features in the test sample. The one or more reporters may be individually selected from the group consisting of plastic micro-spheres, colloidal gold beads, silica beads, glass beads, latex beads, polystyrene beads, magnetic beads, and fluorescent beads. Also in this method, the step of detecting the return beam may form a plurality of analog signals, and the step of processing comprises converting the analog signals into a digitized signal. In this particular embodiment, the step of processing involves a signal processing system that may include an external analog-to-digital converter with or without a buffer amplifier. Alternatively, the signal processing system may be provided with programmable digital signal processing circuitry and/or related audio processing circuitry. 
     In many implementations of this particular method, the step of processing the detected return beam may include the further steps of (1) summing a first subset of the plurality of analog signals to produce a sum signal, (2) combining one of the first subset and a second subset of the plurality of analog signals to produce a tracking error signal, (3) obtaining information used to operate an optical disc drive from the tracking error signal, (4) converting the sum signal to a digitized signal, and (4) outputting the digitized signal. In these implementations, the step of outputting may involve displaying the digitized signal on a monitor or playing the digitized signal as sound using speakers. 
     In accordance with yet still additional aspects of this invention, there is provided a kit for the detection of an investigational feature in a test sample. The kit includes a carrier compartmentalized to receive one or more optical discs. The kit may further include one or more containers, the containers having one or more agents selected from the group consisting of isolated nucleic acids, antibodies, proteins, reagents, and reporters. The kit of may further be provided with at least one optical bio-disc according to the present invention, and/or a setup optical disc. 
     The kit may further include a buffer amplifier card, the card being adapted to retrofit into an optical disc drive. The kit may alternatively include a modified optical disc drive. 
     According to still further aspects of this invention, an optical analysis disc for detection of a signal element is provided. This disc includes a substrate layer, an operational layer associated with the substrate layer, the operational layer having operational information encoded therein, and a signal element positioned relative to the operational layer, the signal element and the operational layer having optical or magnetic characteristics selected to provide a predetermined contrast therebetween to thereby provide a return signal indicative of distinctions between information associated with the operation layer and characteristics of the signal element. The optical or magnetic characteristics include but are not limited to, electrical or magnetic polarization state or irradiance of the signal element and/or the operational layer. 
     In accordance with yet still additional aspects of the present invention, there is provided an optical analysis disc for use in imaging a biological or medical investigational feature. This disc includes a substrate, an operational layer associated with the substrate, the operational layer having encoded operational features positioned relative to each other at a specified track pitch, and an investigational feature positioned relative to the operational layer, the investigational feature selected to be larger in size than a corresponding operational feature and at least as large in size as one-half of the track pitch to thereby provide at least one scan of the investigational feature as an incident beam tracks along the operational features. In this embodiment, rotational speed of the disc may be controlled to produce a higher quantized resolution in the digitization of a return signal generated by the disc. This disc may also advantageously include logic to provide random access to preaddressed locations on the disc. 
    
    
     
       BRIEF DESCRIPTION OF DRAWING FIGURES 
       Further objects of the present invention together with additional features contributing thereto and advantages accruing therefrom will be apparent from the following description of the preferred embodiments of the invention which are shown in the accompanying drawing with like reference numerals indicating like components throughout, wherein: 
         FIG. 1  is a cross-sectional view of typical single-layer CD or CD-like disc and a schematic representation of a reader associated therewith; 
         FIG. 2  is a side cross-sectional view of the disc shown in  FIG. 1  at greater magnification; 
         FIG. 3  is a perspective view of the surface of a CD-R disc with wobble grooves; 
         FIG. 4  is a schematic representation of an optical disc detector and associated electronics that use three beams for tracking, focusing, and reading; 
         FIG. 5  is a plan view that illustrates the position of beams from a typical three-beam pickup relative to a track on an optical disc; 
         FIG. 6  is a block diagram of a known optical disc reader; 
         FIG. 7  is a functional block diagram of a conventional digital signal processing circuit; 
         FIG. 8  is a block diagram of a chip set of a generic optical disc reader, modified according to one aspect of the present invention to monitor signals for determining the presence of investigational features or structures on an optical analysis disc; 
         FIG. 9A  is a pictorial representation and block diagram illustrating alternative embodiments of the present invention directed to processing the high frequency, tracking, focusing, audio, or other signals of a disc drive and displaying or outputting results relating thereto; 
         FIG. 9B  is an enlarged detailed perspective view of the section indicated in  FIG. 9A  showing a coordinate reference system used for purposes of 3 dimensional orientation; 
         FIG. 10  is a flow chart depicting a known process for fabricating optical discs and then later reading the optical discs; 
         FIG. 11  is a modified path for decoding optical discs according to the present invention; 
         FIG. 12  is a view similar to  FIG. 9A  showing the optical disc assembly and investigational features in conjunction with the optical components and return beam of an optical disc reader and drive implemented according to a first embodiment of the present invention; 
         FIG. 13  is a plan view of a disc showing target zones and a hardware trigger; 
         FIG. 14  is a block diagram of an overall drive system according to an embodiment of the present invention; 
         FIG. 15  is a top view of a circuit board including a triggering detection assembly according to another aspect of the present invention; 
         FIG. 16  is an electrical schematic of the triggering circuit shown in  FIG. 15 ; 
         FIG. 17  is a part pictorial, part block diagram showing a disc and a reading system as implemented according to certain aspects of the present invention; 
         FIG. 18  is a block diagram of a board with functionality including a trigger, an amplifier, and detection circuitry for use in various embodiments of the present invention; 
         FIG. 19  is a top plan view of an optical disc drive assembly with the housing removed to show the spindle, the carriage assembly, the optical head assembly, and the ribbon cable or connector which transmits signals to and from the optical head assembly; 
         FIG. 20  is a bottom perspective view of the optical disc drive assembly of  FIG. 19 , illustrating the physical layout of the chip set, related electronic circuitry, and the ribbon connector from the head assembly as unplugged from the circuitry; 
         FIG. 21  is a block diagram illustrating the known optical disc reader of  FIG. 6  as connected to a buffer card according to different embodiments of this invention; 
         FIG. 22  is a top perspective view of an external buffer amplifier card adapted to receive signals from the head assembly of the drive buffer according to a first embodiment of the present invention; 
         FIG. 23  is a perspective view of an alternative embodiment of the external buffer amplifier card illustrated in  FIG. 22 ; 
         FIG. 24  is a graphical representation illustrating the relationship between  FIGS. 24A ,  24 B, and  24 C; 
         FIGS. 24A ,  24 B, and  24 C are electrical schematics of the amplifier stages according to a first embodiment of the buffer cards shown in  FIGS. 22 and 23 ; 
         FIG. 25  is a functional block diagram of a digital signal processing circuit programmably configured as an analog-to-digital converter in accordance with the principles of an alternate embodiment of the present invention as represented in  FIG. 9 ; 
         FIG. 26  is a flow chart illustrating some of the steps involved in detecting investigational elements in accordance with the second embodiment of the present invention illustrated in  FIG. 25 ; 
         FIG. 27  is an exploded perspective view of a reflective bio-disc as utilized in conjunction with the present invention; 
         FIG. 28  is a top plan view of the disc shown in  FIG. 27 ; 
         FIG. 29  is a perspective view of the disc illustrated in  FIG. 27  with cut-away sections showing the different layers of the disc; 
         FIG. 30  is an exploded perspective view of a transmissive bio-disc as employed in conjunction with the present invention; 
         FIG. 31  is a perspective view representing the disc shown in  FIG. 30  with a cut-away section illustrating the functional aspects of a semi-reflective layer of the disc; 
         FIG. 32  is a graphical representation showing the relationship between thickness and transmission of a thin gold film; 
         FIG. 33  is a top plan view of the disc shown in  FIG. 30 ; 
         FIG. 34  is a perspective view of the disc illustrated in  FIG. 30  with cut-away sections showing the different layers of the disc including the type of semi-reflective layer shown in  FIG. 31 ; 
         FIG. 35  is a partial cross sectional view taken perpendicular to a radius of the reflective optical bio-disc illustrated in  FIGS. 27 ,  28 , and  29  showing a flow channel formed therein; 
         FIG. 36  is a partial cross sectional view taken perpendicular to a radius of the transmissive optical bio-disc illustrated in  FIGS. 30 ,  33 , and  34  showing a flow channel formed therein and a top detector; 
         FIG. 37  is a partial longitudinal cross sectional view of the reflective optical bio-disc shown in  FIGS. 27 ,  28 , and  29  illustrating a wobble groove formed therein; 
         FIG. 38  is a partial longitudinal cross sectional view of the transmissive optical bio-disc illustrated in  FIGS. 30 ,  33 , and  34  showing a wobble groove formed therein and a top detector; 
         FIG. 39  is a view similar to  FIG. 35  showing the entire thickness of the reflective disc and the initial refractive property thereof; 
         FIG. 40  is a view similar to  FIG. 36  showing the entire thickness of the transmissive disc and the initial refractive property thereof; 
         FIG. 41  is a cross sectional side view of an optical disc assembly including a light refractive cover and investigational features according to the present invention; 
         FIG. 42  is a plan view showing a typical three-beam system projecting onto three tracks of the disc; 
         FIG. 43  is a plan view of three beams relative to three tracks, one of which has an investigational feature positioned thereon according to the present invention; 
         FIG. 44  is a graph depicting a signal that corresponds to an operation feature such as a pit or land including discernable changes as exploited by the present invention; 
         FIGS. 45 and 46  are graphs depicting changes in signals produced by operational features encountered on the disc; 
         FIG. 47  is a section view of a bio-disc according to the present invention that shows a micro-fluidic channel; 
         FIG. 48  is a representative graph of the change in reflectivity of materials with thickness that is exploited according to the present invention; 
         FIG. 49  is pair of graphs depicting an envelope of fluctuations of an analog readout signal that has been enlarged by reaction in a micro-fluidic channel according to the present invention; 
         FIG. 50  is a plan view of a bio-disc and corresponding readout of test sample signals according to the present invention; 
         FIG. 51  is a cross-sectional side view of an optical bio-disc including bead reporters as utilized in conjunction with the present invention; 
         FIG. 52A  is a graphical representation of two 6.8 μm blue beads positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 52B  is a series of signature traces derived from the beads of  FIG. 52A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 53A  is a graphical representation of two 6.42 μm red beads positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 53B  is a series of signature traces derived from the beads of  FIG. 53A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 54A  is a graphical representation of two 6.33 μm polystyrene beads positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 54B  is a series of signature traces derived from the beads of  FIG. 54A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 55A  is a graphical representation of a 5.5 μm glass bead positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 55B  is a series of signature traces derived from the bead illustrated in  FIG. 55A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 56A  is a graphical representation of a 4.5 μm magnetic bead positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 56B  is a series of signature traces derived from the bead of  FIG. 56A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 57A  is a graphical representation of two 4.0 μm blue beads positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 57B  is a series of signature traces derived from the beads of  FIG. 57A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 58A  is a graphical representation of a 2.986 μm polystyrene bead positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 58B  is a series of signature traces derived from the bead illustrated in  FIG. 58A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 59A  is a graphical representation of two 2.9 μm white beads positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 59B  is a series of signature traces derived from the beads of  FIG. 59A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 60A  is a graphical representation of four 2.8 μm magnetic beads positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 60B  is a series of signature traces derived from the beads of  FIG. 60A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 61A  is a graphical representation of a mixture of beads including 2.8 μm magnetic beads, 4.0 and 6.8 μm blue polystyrene beads, and different sized silica beads positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 61B  is a series of signature traces derived from the cluster of beads illustrated in  FIG. 61A , the traces being derived from an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 62A  is a graphical representation of two 2.9 μm white fluorescent polystyrene beads positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 62B  is a series of signature traces derived from the beads of  FIG. 62A  utilizing a DC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 63A  is a graphical representation of two 2.9 μm white fluorescent polystyrene beads positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 63B  is a series of signature traces derived from the beads of  FIG. 63A  utilizing a DC coupled and buffered “A” signal from the optical drive according to the present invention; 
         FIGS. 64A and 64B  are cross-sectional side views similar to  FIG. 51  showing the biochemical interaction between the bio-disc and the reporter beads in greater detail; 
         FIG. 65  is a cross-sectional side view of an optical bio-disc including a proximally positioned red blood cell as the investigational feature interrogated by the read beam of the optical disc drive assembly according to the present invention; 
         FIG. 66A  is a graphical representation of a proximally positioned red blood cell approximately 6.0 μm in diameter positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 66B  is a series of signature traces derived from the red blood cell of  FIG. 66A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 67A  is a graphical representation of a proximally positioned red blood cell approximately 6.0 μm in diameter positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 67B  is a series of signature traces derived from the red blood cell of  FIG. 67A  utilizing a DC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 68  is a cross-sectional side view of an optical bio-disc including a distally positioned red blood cell as the investigational feature interrogated by the read beam of the optical disc drive assembly according to the present invention; 
         FIG. 69A  is a graphical representation of two distally positioned red blood cells approximately 6.0 μm in diameter positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 69B  is a series of signature traces derived from the red blood cells of  FIG. 69A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 70A  is a graphical representation of two distally positioned red blood cells approximately 6.0 μm in diameter positioned relative to the tracks of an optical bio-disc according to the present invention; 
         FIG. 70B  is a series of signature traces derived from the red blood cells of  FIG. 70A  utilizing a DC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 71  is a perspective top view an optical inspection disc with a portion of the top cap cut away to illustrate a gnat&#39;s wing positioned in an inspection channel according to the present invention; 
         FIG. 71A  is an enlarged top view of the indicated portion of  FIG. 71  showing in greater detail the gnat&#39;s wing, inspection channel, information storage tracks of the disc, and a focused spot of an incident beam on the tracks of the optical inspection disc according to this embodiment of the present invention; 
         FIG. 72  is a cross-sectional side view taken perpendicular to a radius of the optical inspection disc of  FIG. 71  including the gnat&#39;s wing as the investigational feature interrogated according to the present invention by the read beam of an optical disc drive assembly; 
         FIG. 73A  is a graphical representation of a lateral section of the gnat&#39;s wing of  FIGS. 71A and 72  as positioned in the inspection channel relative to the tracks of an optical inspection disc according to the present invention; 
         FIG. 73B  is a single signature trace derived from the section of the gnat&#39;s wing of  FIG. 73A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 74A  is a graphical representation similar to that shown in  FIG. 73A ; 
         FIG. 74B  is a series of four consecutive signature traces derived from the section of the gnat&#39;s wing of  FIG. 74A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 75A  is a graphical representation similar to that shown in  FIG. 73A ; 
         FIG. 75B  is a series of consecutive signature traces at moderate density derived from the section of the gnat&#39;s wing of  FIG. 75A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIG. 76A  is a graphical representation similar to that shown in  FIG. 73A ; 
         FIG. 76B  is a series of consecutive signature traces at higher density derived from the section of the gnat&#39;s wing of  FIG. 76A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention; 
         FIGS. 77A ,  77 B, and  77 C are pictorial representations of the gnat&#39;s wing of  FIGS. 71A and 72  as rendered by methods according to the present invention respectively utilizing either an AC coupled and buffered HF signal, a DC coupled and buffered “A” signal, or a DC coupled and buffered HF signal from an optical drive assembly; 
         FIG. 78  is a graphical representation illustrating the relationship between  FIGS. 78A and 78B ; 
         FIGS. 78A and 78B  are electrical schematics of a second embodiment of the amplifier stages that may be implemented according to the present invention in the buffer cards shown in  FIGS. 22 and 23 ; 
         FIGS. 79A ,  79 B,  79 C, and  79 D are cross-sectional side views of an optical bio-disc showing a method of detecting investigational features in a test sample. 
         FIGS. 80A ,  80 B,  80 C, and  80 D are cross-sectional side views of an optical bio-disc used in a mixed phase assay to detect investigational features in a test sample; 
         FIGS. 81A ,  81 B,  81 C,  81 D,  81 E, and  81 F are cross-sectional side views of an optical bio-disc showing a method of detecting investigational features in a test sample using ELISA; 
         FIG. 82  is a detailed partial cross-sectional view of the surface of a bio-disc showing reporter beads having specific affinity for antigens bound to the surface; 
         FIGS. 83A ,  83 B,  83 C, and  83 D are cross-sectional side views of an optical bio-disc showing a method of using reporter beads to detect investigational features in a test sample; 
         FIG. 84  is a detailed partial cross-sectional view of the surface of a bio-disc showing use of reporter beads, capture probes, and signal probes to detect investigational features in a test sample; 
         FIG. 85  is view similar to  FIG. 84 , showing hybridization of the investigational feature to the capture and signal probes; and 
         FIG. 86  is a schematic depiction of a technique that adds good channel bits to read out from an optical disk to facilitate the detection of bio-bits. 
         FIG. 87A  is a side view of a hybrid optical disc implementation. 
         FIG. 87B  is a top view of a hybrid optical disc implementation. 
         FIG. 88A  depicts a prior art implementation of the objective assembly in consumer CD-R player. 
         FIG. 88B  depicts an implementation of the objective assembly in a CD-R player with an added adjustment lens. 
     
    
    
     DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS 
     The present invention provides methods and an apparatus for detecting operational and investigational structures or features on an optical disc assembly without having to physically modify the processing circuitry and using a conventional disc drive. According to one embodiment of the present invention, one or more signal processing circuits within the conventional disc drive is programmably configured to function as an analog-to-digital (A/D) converter. The A/D converter is used to detect an electronic profile associated with investigational features and structures disposed on a surface of the optical disc assembly. The profiles may be used to determine the relative size, composition, and location of the detected structures. Many different signals from the drive may be utilized to render the desired electronic profiles. Different electronic signals available within the drive may result in different electronic profiles, perturbations, or “signatures” for the same investigational feature. It should be understood, however, that each such signature or signal perturbation is unique and thus may be used as a separate and distinct indicator of the respective investigational feature under consideration. The conventional disc drive may then be programmably returned to its original operating configuration. Processing and imaging software both internal and external to the drive are discussed as related aspects of this embodiment of the present invention. 
     In accordance with another embodiment of this invention, and as an alternative to programmably configuring one or more signal processing circuits within the disc drive to function as an analog-to-digital (AND) converter, an external A/D converter with or without an external buffer card is employed. In these embodiments of the present invention, many different signals from the drive may also be employed to render the desired electronic profiles. As in the prior embodiment, different electronic signals available within the drive may result in different electronic profiles, signal perturbations, or “signatures” for the same investigational feature. It is also understood relative to this embodiment of the present invention, that each such signature is unique and thus may be used as a separate and distinct indicator of the respective investigational feature or attribute thereof under consideration. Processing and imaging software are also related aspects of this embodiment of the present invention. 
     The electrical characterization of light as it enters an objective assembly of an optical disc drive can be utilized to create multi-dimensional images of investigational features on an optical disc. An optical bio-disc can be designed to facilitate the gathering of data and the creation of the image. 
     An optical disc drive may be utilized as an optical disc imaging device to produce multi-dimensional images from a signal element (i.e., a specimen to be imaged) in an optical disc assembly. The energy reflected from the surface of an optical disc or optical disc assembly is gathered on the photo detector in an objective assembly and utilized to reproduce a multi-dimensional image. The optical disc properties (mechanical, logical, and optical) and the optical device properties may be optimized to produce high-resolution multi-dimensional images that in some ways distinctly characterize the signal element. 
     The objective assembly and the optical detector of an optical disc drive can be adjusted to facilitate the collection of high-resolution images of investigational features on the surface of an optical disc. The quad detector inside the objective (or within the optical path of the objective lens) is often organized as depicted by  18  in  FIG. 4 . 
     With reference now to  FIG. 8 , chip set  30  of  FIG. 4  can be supplemented relative to its original configuration by the addition of tap buffers  57 ,  58 , and  59 . These tap buffers provide access to unprocessed analog signals such as HF signal  50 , TE signal  52 , and FE signal  54 , respectively, produced by detector  18 , thereby permitting external instrumentation to receive these signals without interfering with normal drive operation. 
     An alternative modification is the addition of tap buffers to allow the unprocessed signals A though F from detector  18  to be processed by external instrumentation or additional circuitry. From these signals, the HF, TE, FE, or any other combination can be formed. Also, any additional detectors available can provide useful signals in this same manner (e.g., G and H detectors in current state-of-the-art drives). Certain drive circuit designs and detector/amplifier devices allow connection of the instrumentation or additional circuitry directly to the detector without the need for the tap buffers. 
     Referring next to  FIG. 9 , there is shown an optical disc drive  140  according to the present invention. Optical disc drive  140  has disc tray  168 , which is adapted to receive a disc  130  of a type designed to accommodate a wide variety of investigational features. Disc  130  may be an optical bio-disc such as those disclosed in commonly assigned U.S. Provisional Application Nos. 60/252,726 entitled “Bioactive Solid Phase for Specific Cell Capture and Optical Bio-Disc Including Same”; 60/249,391 entitled “Optical Disc Assembly for Performing Microscopy and Spectroscopy Using Optical Disc Drive”; and 60/257,705 entitled “Surface Assembly for Immobilizing DNA Capture Probes and Bead-Based Assay Including Optical Bio-Discs and Methods Relating Thereto.” 
     Known optical disc drives are often packaged within a case that includes both the optical disc drive  140  and one or more processing circuit boards as discussed herein. The basic optical disc drive (e.g., optical disc drive  140 ) provides a variety of signals derived from the optical disc. For example, most optical disc drives provide an HF signal  50  as a basic information signal. Such drives also provide a tracking error signal (TE signal)  52 , a focus error signal (FE signal)  54 , and basic signals from the sensing or laser photo detectors often referred to simply as the A, B, C, D, E, and F signals. In a known type of optical disc drive, these signals are processed in a processing circuit board to provide any correcting signals that may be needed to operate the optical disc drive or derive information signals from the optical disc. Such a processing circuit board is frequently packaged within the optical disc drive and may include, for example, a programmable signal processor, as discussed herein. 
       FIG. 9A  shows five implementations of the present invention. These are identified as implementations I, II, III, IV, and V, respectively as illustrated. It should be understood that each implementation might have several embodiments, all of which accomplish the objects of the present invention. 
     In an embodiment of implementation V of the present invention, the unprocessed HF signal  50  is tapped from the optical disc drive  140  and directed to a modified personal computer or PC  142 . Persons skilled in the art will appreciate in light of these teachings that modified PC  142  may be any suitably adapted and programmed processor, microprocessor, application specific integrated circuit (ASIC) or the like. The modified PC  142  includes software and hardware for processing the HF signal generated from the read beam of the optical drive  140  which is modulated as a function of encountering one or more investigational features on or in any one or more of a number of different layers, substrates, or surfaces forming disc  130 . The same read beam is also modulated in a conventional manner by encountering or reading operational features in disc  130 . Such operational features typically include pits and lands as in a pre-recorded CD-like disc or marks and spaces formed by dyed and undyed areas in a recordable disc such as a CD-R. The pits and lands, or marks and spaces, embody encoded information in the nature of data, program, video, and/or audio according to any one of a number of schemes for encoding such information. 
     With modified PC  142 , the optical disc drive  140  preferably includes a buffer amplifier (not shown for clarity) to provide an amplified replica of the HF signal so that the actual HF signal is not distorted by being excessively loaded. The amplified replica of the HF signal (or the actual HF signal itself, if need be) is coupled to modified PC  142  by a cable. The software and hardware for processing the HF signal in the modified PC  142  includes an analog-to-digital converter (ADC) as part of modified PC  142 , preferably a data acquisition board or module that includes a suitable ADC (e.g., with sample rates from 8 MHz to 40 MHz). The ADC digitized sampled data is stored in the PC&#39;s RAM, and processed by the PC under control of the PC&#39;s software. 
     Modified PC  142  may advantageously include a keyboard  144 , a monitor  146 , and speakers  148 . After the modified PC  142  processes the raw HF signal in a desired manner, characteristic aspects of the investigational feature (as discussed below) may be displayed on the monitor  146 . The monitor  146  and speakers  148  may also be employed to display conventional video or audio encoded on disc  130 . Implementation V of the present invention will be hereinafter referred to as the “modified PC implementation” for purposes of convenience and clarity. 
     In an embodiment of implementation III of the present invention illustrated in  FIG. 9A , the optical disc drive  140  is packaged with a processing circuit board that includes a programmable DSP  32  (similar to the DSP in  FIG. 8 ) and an analyzer  154  that operates in combination with a PC  158 . PC  158  includes software, and hardware controlled by the software, implemented to accommodate analysis of investigational features. Analyzer  154  may include another programmable DSP, a programmable microprocessor, application specific integrated circuit (ASIC) or the like implemented to perform functions in support of a biological, chemical, or biochemical investigation. Programmable DSP  32  includes an ADC to digitize the HF signal (or other signal). Analyzer  154  may simply provide a count of the number of times a voltage level exceeds a threshold. Alternatively, analyzer  154  may identify voltage variations (e.g., double peaks, etc.) or other waveforms that are characteristic of investigational features. In any event, programmable DSP  32  performs the highest bandwidth functions, PC  158  performs the lowest bandwidth functions, and analyzer  154  performs functions of intermediate bandwidth. Persons skilled in the art will appreciate in light of these teachings that functions of analyzer  154  may be subsumed into the capabilities of programmable DSP  32 , PC  158  or both. Persons skilled in the art will also appreciate in light of these teachings that PC  158  may be any suitably adapted and programmed processor, microprocessor, application specific integrated circuit (ASIC) or the like. Aspects of this alternative implementation are described in further detail herein below. For purposes of convenience and clarity, implementation III of the present invention will hereinafter be referred to as the “DSP implementation.” 
     According to an embodiment of implementation I of this invention, a tap-off of the HF signal, as buffered by the tap buffer  57  shown in  FIG. 8 , from drive  140  may be directed to an external analog-to-digital converter  150  (ADC  150 ) as shown in FIG.  9 A. As with the modified PC embodiment, the optical disc drive  140  preferably includes buffer amplifier  152  to provide an amplified replica of the actual HF signal so that the actual HF signal is not distorted by being excessively loaded. The amplified replica of the actual HF signal (or the HF signal itself, if need be) is coupled to ADC  150 . Alternatively, any one of a variety of different signals or signal combinations (e.g., the TE and FE signals or the A, B, C, D, E and F signals) may be tapped off of the drive  140  as illustrated. Aspects of this alternative implementation are also described in further detail herein below. For purposes of convenience and clarity, this embodiment of the present invention will hereinafter be referred to as the “A to D embodiment” of implementation I. The A to D embodiment may be modified to include external buffer amplifier card  152  illustrated as implementation  11  in  FIG. 9A . 
     With continuing reference to  FIG. 9A , implementation IV of the present invention illustrates that the audio output of the optical disc drive  140  (i.e., the audio signal) may be utilized, modified, or augmented to produce a sound when the interrogation beam of the drive encounters an investigational feature or attribute. For example, a disc may be pre-recorded with digital silence yet a sound is produced when the read beam “reads” or detects an investigational feature. In this manner, different investigational features may produce discernibly different sounds or tones. Alternatively, the disc may include a sound track that would be interrupted by the formation or presence of an investigational feature blocking the encoded sound information. These embodiments of the present invention may be generally grouped into three different categories, approaches, or techniques. The first includes using the existing sound card that is currently available and usually packaged in many drive assemblies, for example, an audio CD player. Such a sound card generally produces an analog sound signal, but may also give access to a digital signal representative of the sound. The second approach is directed to internally modifying the audio circuitry that exists in such current drive assemblies to provide the analog or digital signal. The third alternative approach or technique according to the present invention, is to provide an external sound module (depicted as audio processing  156  in  FIG. 9A ) that interfaces with the disc drive assembly  140 , processing software, and an audio output device such as the pair of speakers  148 . Implementation IV of the present may generally be referred to as the “audio” implementation. 
     All of the different implementations illustrated in  FIG. 9A , except the modified PC implementation (V), would typically include a conventional PC  158  for functionality described in further detail below. The modified PC implementation would inherently include a PC, and would be modified as to its inputs. However, persons skilled in the art will appreciate in light of these teachings that PC  158  may be any suitably adapted and programmed processor, microprocessor, application specific integrated circuit (ASIC) or the like. 
     Commonly assigned U.S. patent application Ser. No. 09/421,870 entitled “Trackable Optical Discs with Concurrently Readable Analytic Material” (hereinafter the &#39;870 application) discloses coupling an oscilloscope to the HF or RF signal for detecting the dual peak profiles associated with investigational structures while acquiring the encoded information needed to operate the disc drive. These peaks appear as a result of changes in reflectance as the light beam traverses investigational structures or reporters on the optical disc surface. Such electronic profiles may be advantageously used to detect and discriminate among structures under investigation. 
     An embodiment of implementation  11  shows an analog-to-digital (A/D) converter  150  (ADC) connected to the HF signal through buffer  152 . Implementation II may, for example, determine the number of dual peaks encountered (and thus the number of investigational structures or reporters) on any portion of the optical disc. ADC  150  forms digitized samples of the analog HF signal (or other suitable signal), and forms the samples at a sample rate fast enough to capture the characteristics of the peak profiles that are associated with the investigational structure. The magnitude and/or duration of the digitized peak signals may be interpreted by an associated application program to determine the relative size, composition, and location of the detected structures. 
     Operational Functions 
     Light gathered, reflected, or generated from operational features on disc  130  ( FIGS. 9A and 12 ) and processed by components in objective assembly  10  ( FIG. 1 ) are projected onto detector  18  and create electrical signals that are used by servo circuitry  34  ( FIG. 6 ) to provide operational function to the drive. These patterns provide information that allows objective assembly  10  to focus above a focal plane in disc  130  and track operational features (e.g., pits, grooves, lands) that allow objective assembly  10  to be moved along the information tracks associated with the operational surface of the disc assembly. 
     The operational functions of a drive and the signal that directs the drive to perform those operational functions may be utilized to reproduce a multi-dimensional image. These operational functions include, but are not limited to, focusing, tracking, and synchronization. The sum of all of the energy reflected and/or created from the interaction of the signal element with the light emitted from the objective assembly is often referred to as the HF (high frequency) or RF signal. If the photo detector in the objective assembly is organized in a quadrant (as depicted by  18  in  FIG. 4 ), then the signal is referred to as the quad sum signal. This summed signal contains most of the information necessary to reproduce the image through algorithmic manipulation. The other components of the photo detector will produce signals that may be independently measured to produce additional information or operational signals. For example, the energy gathered in the quad detector of an optical disc drive may be organized to produce operational functions as follows:
 
 A+B+C+D=HF  or Quad Sum (provides sync. for pits)
 
 A+D− ( B+C )=Tracking (push-pull technique) (sync. for grooves)
 
 A+C− ( B+D )=Focusing (astigmatic technique)
 
 E−F= Tracking (outrigger technique)
 
     These photo detector component signals may be used independently or in any combination to produce characteristic information about the signal element or signal elements. In most embodiments an algorithmic interaction is necessary in software to reproduce characteristic imaging. The quad detector is the most common in the current market, however a detector distribution that contains more than 4 to 6 components may also be used to enhance characterization. Also, the optical path may be configured in the device to provide signal characterization with coherent, partially coherent, or non-coherent light. 
     Signal responses may be gathered directly or indirectly from the operational signals in the optical disc drive. In one embodiment of the imaging aspects of this invention, an operational signal is directly amplified, digitized, or sampled (bit resolution, sampling rate) and then algorithmically adjusted through software to produce a characteristic image of the signal element. The operational signals may also be electrically manipulated before or after they are digitized. An operational signal may be filtered, amplified, or summed with another signal component before it is digitized in order to produce a characteristic, non-random, or correlative response. For example, a signal may be measured or characterized by an external electrical manipulation such as a signal analyzer. A signal may show a non-random, correlated event when its response is filtered, amplified, or mathematically combined with other signals (e.g., asymmetry, push pull, cross-talk, radial noise, etc.). 
     Signals produced from investigational or non-operational features may also be utilized independently or in combination to produce characteristic images of the investigational feature under study. The signal and logical responses produced by the optical disc drive may also be used to reproduce a characteristic of a signal element or investigational feature. This is somewhat different than the utilization of the signals performing the necessary operational characteristics. A digital signal, analog signal, logical response, optical response, or mechanical response may be gathered from an optical disc drive to characterize the signal element or investigational feature. For example, a signal element with a specific optical or physical property will interact with light in such a way that a characteristic energy pattern or energy distribution is created. This characteristic distribution or pattern on the photo detector may be monitored and measured as a response without adversely affecting the operational functions of the drive. 
     In one exemplary embodiment, an objective assembly in an optical disc drive will interface with the operational features on a surface of an optical disc assembly. This interaction may include the support of all of the operational functions or it may include the suspension of one or more of the operational functions in a predefined “Zone” of the disc. The interaction of the incident beam from the objective assembly with the operational surface and investigational features will produce signal responses in the HF signal, the tracking signal, and the focusing signal. The focusing signal including operational information and information about characteristics of an investigational feature, may be used with an electrical servo circuit to support a response to the movement of the objective assembly within a direction that we will refer to as the “Z” direction, as shown in  FIG. 9B . The tracking or push-pull signal may be used with an electrical servo circuit to support a response to the movement of the objective assembly in a direction that we will refer to as the “X” direction illustrated in  FIG. 9B . The HF signal, DPD signal, or quad sum components may be used to support a response to the movement of the objective assembly in a direction that we will refer to as the “Y” direction. In this way we can gather a 3-dimensional (XYZ) response from the interaction of the incident beam with a signal element or investigational feature  136  by using standard operational responses of the objective assembly. 
     The signal element or investigational feature  136  covers an area in the disc that interacts directly or indirectly with an operational feature that provides a tracking signal. The signal element may be distal relative to the operational features such as, for example, in a transmissive or semi-reflective disc as described below in further detail. Alternatively, the signal element may be removed from areas having full operational functionality such as in a separate “Zone” or “mirror band” formed in or on the disc wherein at least some of the operational functionality has been removed. The signal element may be on a focal plane that is physically removed from an interference pattern producing other operational signals (focus and/or tracking and/or sync.) The signal element should provide a measurable contrast or energy distribution. This contrast may be provided by the difference between the reflective properties of the operational structure (focal plane) and the reflective properties of the signal element. 
     The signal element or investigational feature may be less reflective than the operational plane thus providing a decreasing energy sum to the photo detector. The signal element may have the same or similar reflective properties as the operational plane (or focal plane) but provide a diffractive or phase cancellation, or phase enhancement, response that provides a decreasing signal level in the photo detector. The signal element may be more reflective than the operational plane thus providing an increasing signal level in the photo detector sum signal. The design of the optical disc drive and the design of the optical disc assembly operational features may be enhanced to optimize imaging capabilities. 
     The operational plane that provides a focal plane can be designed to provide maximum contrast or enhancement to the laser/signal element interaction. As would be understood by one of ordinary skill in the art, focal plane includes the point of greatest reflectively at any particular time during laser focusing. If the focal plane is more reflective than the signal element or investigational feature, then it is desirable to enhance the interference or phase contrast characteristics of the design. If the focal plane is less reflective than the signal element, then it is desirable to enhance the reflectivity and linear signal response of the signal. The focal resolution is dependent on the wavelength of the laser in the objective assembly, the numerical aperture of the focal lens, the bandwidth of the focusing servo loop, and the optical properties of the optical disc assembly. 
     In the design of the disc system according to the present invention, it is important to create strong signal recognition patterns that differentiate operational function from signal element characterization. The light reflected, absorbed, or transmitted through the disc should characterize the signal element with as much detail and magnitude as possible. 
     The response in the reflected or transmitted light can be influenced by the signal element in many ways. The signal element itself can also be designed with the operational characteristics of the disc to provide a high degree of contrast in the transmitted or reflected light. The energy level, energy distribution, and polarization state of the light can be influenced by the design of the signal element and its relationship to the optical properties of the focal plane in the disc. 
     One embodiment directed to signal element selection and design, is to create a signal element that has a reflectivity that is vastly different from the reflectivity of the focal plane of the disc. The reflectivity of the signal element is thus designed to be very high or very low in comparison to the reflectivity of the disc. This will produce a high amount of signal contrast and a strong characteristic signal. 
     The difference in reflectivity between the focal plane and the signal element can be generated in many ways. These include, but are not limited to, the following: 
     1. The material in the signal element can have a lower or higher reflectivity and thus produce a lower or higher signal level than the surrounding plane of the disc. 
     2. If the signal element is smaller than the beam size, an interference pattern is created and the size of the signal element can create a destructive or additive component to the signal. 
     3. The signal element may be activated by an energy source that creates a state condition that results in a lower or higher reflectivity than the surrounding area (phase change materials). 
     An alternative embodiment directed to signal element selection and design involves the use of materials and states that interfere with the polarization state of the light transmitted or reflected through the disc. The signal element can be designed to have an optical or magnetic property that has a contrasting effect on the polarization state of the light interacting with the disc assembly. There are many ways that this embodiment can be created in the disc. These include, but are not limited to, the following: 
     1. A signal element can be designed that is transparent but birefringent or diChroic in nature. The optical components of the detector will transmit, reflect, or absorb the resulting signal based on its state. 
     2. A signal element may be designed to produce a magnetic orientation that provides a contrasting polarization state in the light. 
     A third group of embodiments directed to signal element selection and design involves the use of optical or interference properties that interfere with the energy distribution of light that is transmitted or reflected through the disc. The signal element can be designed to diffract the light in such a way that it creates a higher energy response from a non-intrinsic detector. A measurable or detectable contrast is provided in the resulting signal by the area of light on the surface of the detector. 
     A fourth group of embodiments directed to signal element selection and design involves the use of chemical luminescence. The signal element or surface of the disc can be designed to emit energy in a secondary active state. This involves, for example, the use of fluorescent or phosphorescent markers or dyes applied to the signal element and/or an appropriate disc surface. Suitable signal elements for this group of embodiments include, but are not limited to, beads and cells such as blood cells, for example. The state is activated by the incident energy on the disc assembly. A contrasting energy is thereby created and exists in the transmitted or reflected return signal. 
     The present invention is thus directed to an optical analysis disc for detection of a signal element. The disc preferably includes a substrate layer and an operational layer associated with the substrate layer. The operational layer has operational information encoded therein. According to this aspect of the present invention, the analysis disc further includes a signal element positioned relative to the operational layer. The signal element and the operational layer have optical or magnetic characteristics selected to provide a predetermined contrast therebetween to thereby provide a return signal indicative of distinctions between information associated with the operation layer and characteristics of the signal element. 
     Incident Light 
     The wavelength of light emitted by laser (i.e., light source  19   FIGS. 1 and 12 ) utilized in objective assembly  10 ,  FIG. 1 , of the optical disc drive will have an effect on the resolution of the optical disc system. In theory, the smallest signal element or investigational feature that may be detected by an objective assembly (at the element/laser interface) with a wavelength λ will be λ/2NA, where NA is the numerical aperture of the objective lens. At any instant in time, the investigational feature or signal element, at the laser/plane interface may be larger or smaller than the field that is covered by the beam at or near the focal point. A signal element that is larger than the laser beam coverage at the laser/signal element interface will produce more characteristic signals than a signal element that is smaller than the laser coverage. 
     The wavelength of the laser should be as small as possible to enhance the resolution of the signal response. This will result in greater detail and characterization capabilities for smaller signal elements and investigational features. Shorter wavelengths produce smaller focal spots on the focal plane of the optical disc assembly. Therefore, a shorter wavelength will produce a higher spatial resolution in the imaging device. An objective assembly with a high numerical aperture will provide less focal distance and greater diffraction capability. 
     The drive should have very little mechanical or electrical influence on the signal response or signal consistency of the laser/signal element interface. In certain circumstances, the drive operation may have an influence if designed to do so (e.g., electrical coupling, sync enhancement, signal gain control settings AGC, signal power level setting). 
     Extracting Information from an Optical Disc 
     Referring now to  FIG. 10 , the conventional process of encoding video, data, or audio information such as music on a disc and then later decoding signals from the disc to recover the audio, video, or data is illustrated. The audio, video, or data signal is sampled at block  70 , quantized at block  71 , encoded into a standard format at block  72 , and modulated onto a master disc at block  73 . Replicated discs are then mass manufactured at block  74 . In a disc reader, signals derived from a manufactured disc are processed through a signal processor at block  75 , demodulated at block  76 , then decoded at block  77  to recover the original audio, video, and/or data. This output is then displayed on a monitor and/or played on a pair of speakers for a user&#39;s use and enjoyment. 
     With reference next to  FIG. 11 , an optical disc decoding system is shown modified in such a way that some functionality in the system is removed. The path is modified to remove the Demodulation and Decoding operations (blocks  76  and  77  of  FIG. 10 ) and provide a raw digitized signal to a computer to effectively characterize a group of signal elements of investigational features on a surface of the optical disc assembly. 
     In addition to pre-recorded optical discs, a variety of recordable optical discs are currently available. A recordable master includes a variety of operational features that are designed for use during the recording operation and not the reading operation. Table 1 below summarizes these operational differences. 
     
       
         
           
               
               
               
               
             
               
                 TABLE 1 
               
               
                   
               
               
                   
                   
                   
                 Reading or 
               
               
                   
                   
                 Recording 
                 Playback 
               
               
                 Disc Type 
                 Function 
                 Properties 
                 Properties 
               
               
                   
               
             
            
               
                 CD-R 
                 Focus 
                 Surface Properties 
                 Surface 
               
               
                 CD-RW 
                   
                   
                 Properties 
               
               
                   
                 Tracking 
                 22.05 KHz Wobble 
                 Pits or Marks 
               
               
                   
                   
                 Groove 
               
               
                   
                 Synchronization 
                 22.05 KHz Wobble 
                 Pit Patterns 
               
               
                   
                 (speed control) 
                 Groove 
                 (Marks) 
               
               
                 DVD-R 
                 Focus 
                 Surface Properties 
                 Surface 
               
               
                 DVD-RW 
                   
                   
                 Properties 
               
               
                 DVD-RAM 
                 Tracking 
                 140 or 160 KHz 
                 Pits or Marks 
               
               
                 DVD + RW 
                   
                 Wobble Groove 
               
               
                   
                 Synchronization 
                 140 or 160 KHz 
                 Pit Patterns 
               
               
                   
                 (speed control) 
                 Wobble Groove 
                 (Marks) 
               
               
                   
               
            
           
         
       
     
     As indicated above, the decoder or servo system of a CD, CD-R, or DVD player can be used to provide a count, correlation, or characterization of a chemical response in the focal or operational feature plane of a disc. Other responses or raw signals from the drive chip set that quantify the signal magnitudes from an investigational feature or signal producing element include the high frequency signal (HF) (AC or DC coupled), the tracking error signal (TE), the focus error signal (FE), the Automatic Gain Control Setting (AGC), the push-pull tracking signal ((B+C)−(A+D)), the CD tracking signal (E−F), the CD-R tracking signal ((A+D)−(B+C)), the focus signal ((A+C)−(B+D)), the differential phase detector signal (DPD) ((A+B)−(C+D)), the power monitor signal from the back of the laser, and the audio signal. Additional signals, which may be employed with the present invention, include the individual signals from the quad detector, A, B, C, and D, or side detectors E and F. 
     A trend in current conventional drives is to use a high-density photo detector array in place of the typical quad detector. The methods of the present invention may also be advantageously utilized in conjunction with such array detectors currently becoming available in the market. These arrays include, for example, individual signals A, B, C, D, E, F, G, . . . Z. Each of these signals, or combinations thereof, may be advantageously employed according to different embodiments of this invention to obtain the desired electronic profiles, signatures, or signal perturbations that uniquely characterize the signal element, investigational feature, or attribute of interest. 
     Imaging Techniques and Operational Features 
     The operational features and layout of the optical bio-disc assembly can be designed to optimize the imaging operation. The optical disc assembly may be further designed in specific areas or “zones” to enhance the detection and characterization of signal elements or investigational features and to provide higher signal resolution with specific laser interface properties. 
     The operational features most often provide tracking signals that allow the objective assembly to move from the inner to the outer area of the optical disc assembly. A smaller track pitch, or spacing between the operational features, will yield a greater resolution because of the corresponding increase in the number of responses associated with the investigational feature. By providing an operational feature that is smaller than the signal element and a track pitch that is comparable to the signal element, multiple electrical scans can be gathered from the laser/signal element interaction. The number of potential scans of a signal element at a fixed position on or near the operational plane (focal plane) is increased as the track pitch is decreased. The accuracy with which the location or position of the investigational feature or signal element on the disc can be resolved, is increased as the operational features are made smaller given a fixed signal element size. This location accuracy is herein generally referred to as “positional resolution”. This holds true with a consistent objective assembly/operational feature interface. The typical track pitch for a CD is 1.5–1.7 μm, for a DVD is 0.73–0.75 μm, and for a DVD-RAM is 0.35 μm. 
     The operational features also provide synchronization information that affects the speed of rotation of the disc and thus the duration during which the laser interacts with the signal element. Lower speeds produce higher quantized resolution in the digitization of the signal by the A/D converter. This increases the sampling resolution of the system. As the rotational speed is increased, the sampling frequency and bit resolution must be increased in a corresponding manner to achieve a consistent sampling resolution. The typical track speed for a CD is 1.2 m/sec, and for a DVD is 3.49 m/sec. 
     The optical disc assembly or a section of the optical disc assembly may be designed specifically for imaging. A disc with a slow rotational speed, a tight track pitch, and an optimized focal plane will provide an exceptional response for imaging purposes. An optimal disc or disc component design would also include logic to provide random access to preaddressed investigational locations of positions on the disc. The logic may be encoded in the operational features of the disc or alternatively formed by physical markings on the disc assembly. The logic may be designed to accommodate the investigational protocols for specific assays assigned to different zones on the disc. Such investigational protocols include, but are not limited to, sampling rate, bit resolution, rotational speed, focus and tracking off-set, laser power, laser light wavelength, rotational direction, acceleration, deceleration, and any other system interactions required by a particular assay. 
     An optical disc system can be created with (1) operational features or tracking features having a very tight track pitch to facilitate the tangential resolution of the data gathered (e.g., DVD-0.74 μm); (2) logic and hardware that provide for land/groove or land/pit tracking, enhancing the tangential resolution (e.g., DVD-RAM or MO); (3) logic or operational features that provide for slower disc revolution speed (shorter pits or wobbled grooves) to provide higher signal detail; (4) disc or lens component thickness&#39; that may be made to promote a smaller or larger spot on the focal plane of the disc assembly (the components to be imaged may be slightly out of the exact focal plane or they may provide a new focal position for the objective assembly); (5) hardware providing a lower wavelength laser to enhance resolution (e.g., DVD 635–650 nm, HD-DVD approximately 400 nm); (6) a sampling system that provides a higher sampling frequency or higher sample bit resolution to enhance the imaging; (7) software to provide the processing functionality of mathematical transforms or operational functions to derive approximations to the imaging; and (8) the disc or lens component positioned laser proximal to the feature that enhances the interaction of the light with the feature (e.g., an SIL-type component for manipulating the evanescent field). 
     In the imaging of an investigational feature as situated on an optical bio-disc, it is desired to produce any measurable contrast between the investigational feature or signal element and the focal plane. This desired contrast can be achieved by use of reflective signal elements or investigational features in combination with a less reflective focal or operational plane. Alternatively, the desired contrast can also be achieved by use of non-reflective signal elements or investigational features in combination with a more reflective focal or operational plane. 
     Optical Disc Drive and Related Disc Formats 
     The optical bio-disc may be implemented on an optical disc including a format such as CD, CD-R, or DVD or a modified version thereof. The bio-disc may include encoded information for performing, controlling, and post-processing the test or assay. For example, such encoded information may be directed to controlling the rotation rate of the disc. Depending on the test, assay, or investigational protocol, the rotation rate may be variable with intervening or consecutive sessions of acceleration, constant speed, and deceleration. These sessions may be closely controlled both as to speed, direction, and time of rotation to provide, for example, predetermined mixing, agitation, or separation of fluids and suspensions with agents, reagents, or antibodies. A disc drive assembly is employed to rotate the disc, read and process any encoded information stored on the disc, and analyze the liquid, chemical, biological, or biochemical component in any assay zone of the disc. The disc drive assembly may also be utilized to write information to the bio-disc. The recording may occur either before or after performing the assay or test. 
     According to another embodiment of the present invention, an optical disc drive chip set is employed as an A/D converter to sample a read beam and thereafter to identify investigational features and structures, and thereafter to characterize such features and structures as unique signal perturbations or electronic signatures. An optical disc decoding system may be modified in such a way that some functionality in the system is removed. The removal of specific features from the decoding path of an optical disc decoder will provide a raw digital signal that effectively characterizes and uniquely identifies investigational features positioned on the surface of the optical bio-disc, on a substrate within the disc, or residing within a chamber or channel formed as a fluidic element of the disc assembly. 
     According to another embodiment of the present invention, a conventional disc drive is employed to identify investigational features and structures. In this case, firmware modifications enable the user to monitor known signals within the disc drive, without the need to modify the electronics or hardware. The value of the AGC signal can be useful as a measuring tool. The AGC functionality tries to ensure that the analog output signal has a consistent range. If the disc drive is used to read binary data, only a high value and a low value are needed. In the case of investigational features, however, values may be desirable over a continuum of ranges. The AGC is high where the signal level is low, and vice versa. The AGC can thus be used as a signal that is representative of the light that is received by the detector, and therefore can be used for measurement and detecting changes in an investigational feature. 
     A CD-R player/recorder of this embodiment adds an adjustment lens to the objective assembly of a commercial optical disc player. A player/recorder that is designed for use in the consumer market for the recording of recordable CD discs can be utilized to detect microscopic structures. The drive is modified at the exit position of the objective assembly. A small refractive optical lens is added to the optical path of a CD-Recordable drive.  FIGS. 88A and 88B  show the addition of this adjustment lens.  FIG. 88A  shows a commercial optical disc player with recordable CD disc  1112 . The shaded area indicates a 1.2 mm polycarbonate layer that helps focus and polarize the beams. In  FIG. 88B , an adjustment lens  1114  is added at the exit position of the objective assembly  1110 . This optical adjustment lens provides the necessary focusing and polarization characteristics to provide for standard operation of the CD-Recordable drive. The adjustment lens will adjust the focusing path and provide the necessary reflection to the diode laser to provide the desired spot size and energy distribution on the surface of the optical disc. The adjustment lens will provide a polarizing phase shift similar to the polarizing shift provided by the 1.2 mm polycarbonate layer in the construction of the optical disc. This layer is absence in the disc  1116  used in the present embodiment. Instead an air-filled layer is used for depositing biological samples for detection and analysis. The characteristics of the adjustment lens can be changed to provide an optimal situation for the detection of bio-bits such as beads, cells, colloidal gold, carbon, or other microscopic markers and reporters associated with an optical disc. The adjustment lens is designed in such a way as to optimize the operational characteristics of each component in the optical path of an optical disc player/recorder. 
     A sampling system is designed and optimized to detect and characterize the electrical responses from the investigational structures and signal elements on the surface of the optical analysis disc. The sampling system monitors and delivers information from the servo control signals discussed previously. The information delivered will include qualitative and quantitative information. 
     The objective assembly of an optical disc player or recorder will send out a modulated or continuous wave laser pulse from a laser diode. It will record the reflected information from the surface of an optical disc on a combination photo detector and will generate four servo signals that provide for the operational requirements (i.e., tracking, focusing, synchronization, and power control). The microscopic structures can be detected and characterized from each, or a combination, of the electrical signals that are generated from the electrical servos. This includes, but is not limited to, the use of all tracking spots on a 3-beam outrigger system to detect and characterize features. 
     The focusing servo signal may be generated from at least 3 focusing techniques: critical angle focusing, Focault or knife-edge focusing, or astigmatic focusing. The tracking servo signal may be generated from at least 4 types of tracking techniques: one beam push-pull tracking, 3 beam outrigger tracking, Differential Phase Detection (DVD), or one beam high frequency wobble tracking. Synchronization is generated from at least three differing methods: bit clock synchronization or bit pattern sync, zoned clocking method (DVD-RAM), or wobbling groove synchronization. Power control is generated from more than 4 methods: power monitoring signal in PCA or CD-R disc, running power control method or real time power control of pulse diode, power or strategy adjustment, or optimum power encoded in wobble groove information. Logic is generated from over 40 known optical disc formats. Logic can perform position sensing, power control, radial and tangential location, layer sensing, density detection, multi-session usage as well as a wide variety of other functions. 
     The optical disc drive servos can be used to detect sizes of investigational features, signal elements, or various structures thereof. The movement of the laser across the bio-bit will result in a signal deflection in the optical disc tracking system servo signal and/or the optical disc focus system servo signal. The deflection in the electrical signal associated with a closed loop signal beam push-pull tracking system or 3-beam outrigger tracking system is used to characterize the bio-bit and can be processed as a quantifiable piece of digital or analog information. The deflection in the electrical signal associated with a closed loop 3-beam astigmatic or closed loop 1-beam Focault focusing system can be used to characterize the bio-bit and can be processed as a quantifiable piece of analog or digital information. 
     As the push-pull tracking system interacts with a spherical bio-bit, the optical assembly is moved in both the horizontal and vertical planes. The movement of the optical assembly in the horizontal plane will be toward the outer or inner radial direction. This will result in a positive or negative deflection of the electrical signal applied to the push pull tracking servo circuit. A low pass or band pass electrical filter may be used to determine the presence and characteristics of the bio-bit. 
     As the 3-beam outrigger tracking system interacts with a spherical bio-bit, the optical assembly will be moved in both the horizontal and vertical planes. The movements of the optical assembly in the horizontal plane will be toward the outer or inner radial direction. This will result in a positive or negative deflection or the electrical signal applied to the differential tracking servo circuit. A low pass or band pass electrical filter may be used to determine the presence and characteristics of the bio-bit. 
     An electrical circuit that is electrically isolated from the tracking servo loop can determine differences in the characteristics of the bio-bits. This electrical circuit may be a series of low pass or band pass filters that are used to isolate and characterize the frequency and magnitude of the deflections in the closed loop tracking system that are caused by the movement of the laser over the bio-bits. The size of the bio-bits can be characterized by the magnitude of deflection of the electrical tracking signal in the push-pull tracking system or the outrigger differential tracking system. The size and shape of the bio-bits may also be characterized by the frequency of the deflection of the electrical tracking signal in the push-pull or differential tracking system. 
     In other embodiments of the present invention, an optical disc assembly with multiple beams read from a disc with multiple layers. One layer/beam pair provides the operational elements such as tracking. At the same time the remaining layer/beam pairs are used for detecting bio-bits. 
     Controlling Drive Functions 
     In order for the optical disc system to correctly operate it must: (1) accurately focus above the operational plane of the optical disc assembly; (2) accurately follow the spiral disc track or utilize some form of uniform radial movement across the disc surface; (3) recover enough information to facilitate a form of speed control (CAV, CLV, or VBR); (4) maintain the proper power control by logical information gathered from the disc or by signal patterns detected in the operational plane of the disc; and (5) respond to logic information that is used to control the position of the objective assembly, speed of rotation, or focusing position of the laser responsible for providing operational requirements. 
     An optical disc objective assembly performs three principal operational requirements by utilizing electrical and logical servos. An objective assembly thus provides an electrical signal to: (1) the focusing servo circuitry, (2) the tracking servo circuitry, and (3) the information processing circuitry. In the case of a CD recordable system, a fourth requirement is necessary to provide power control. In these systems, the objective assembly also provides an electrical signal to the laser power control circuitry (“Signal Monitor”). 
     When a CD-Recordable (CD-R) disc is played back on a CD-Recordable player, it utilizes a “continuous wobbled groove” and a reflective disc surface to provide information to the focusing servo, tracking servo, and power control servo. No features are detected on the surface of the optical disc until a recordable disc is written and contrasting marks have been provided. The quad sum detector will detect light-contrasting structures that are placed on the air-incident surface of a reverse imaged CD recordable disc. These structures will provide characteristic signals that can be detected by electrical monitoring of the quad sum detector. 
     The wobble signal is used to satisfy operational requirements #2 and #3 above. There is a component of the wobble signal referred to as secondary wobble (Bi-phase mark) that is responsible for operational requirement #5. 
     The pit or mark patterns are detectable in both the tracking and HF signals of the optical objective assembly. No signals are generated in the radial plane. By using the CD recordable system, the electrical effects of the biobits is isolated from the tracking requirements of the system. The CD recordable wobble signal is generated in the radial plane and cannot be detected in the HF servo signal. The radial plane is primarily detectable in the tracking signal. Very little information from radial components are detectable in the HF signal. This allows us to isolate the tracking signal from the HF or Quad sum signal. This signal isolation is advantageous to the application of detecting biobits. 
     The effect of biobits on the wobble signal can be described by the following mathematical relationships. On the current CD-recordable system a wobble signal is utilized at a locking frequency of 22.05 kHz or 45.35 msecs. At a linear velocity of 1.2 meters/sec we would compare a single wave of the wobble pattern to a physical component of 54.42 microns. In other words, we are able to detect physical features in the radial plane that are very large. 
     By using this isolation technique we will be able to detect very large features without losing tracking. The successful physical measurement of a biobit can be determined by monitoring the HF and tracking signals simultaneously. If the biobit is small enough an electrical deflection will be noted at the output of the Quad sum or HF signal with no associated electrical impulse noted at the output of the tracking signal. There will, of course be some electrical impulse noted on the tracking signal but it will be very small in comparison. A similar relationship between the HF signal and the Focusing servo signal will be noted. 
     With reference now to  FIG. 12 , there is shown an expanded view of implementation II ( FIG. 9A ) showing the optical disc assembly  130  with bio-bits, signal elements, or investigational features  136  in conjunction with optical disc drive  140 , buffer amplifier card  152 , ADC  150 , PC  158 , and display  146  implemented according to the present invention. In one embodiment, raw detected signals (A, B, C, D, E, and F) are tapped off and fed directly into external buffer amplifier card  152 . In another embodiment, detected signals A, B, C, D, E, and F are processed in the optical disc drive&#39;s drive buffer  151  prior to entering external buffer amplifier card  152 . In yet another embodiment, both tapped off raw signals and signals processed by drive buffer  151  are fed into external buffer amplifier card  152 . Signals exiting external buffer amplifier card  152  enter ADC  150  for further processing according to implementation II ( FIG. 9A ) of the invention. 
     With continuing reference to  FIG. 12 , a drive motor  95  and a controller  96  are provided for controlling the rotation of disc  130 . A hardware trigger sensor  141  may be used. Trigger sensor  141  provides a signal to ADC  150  that allows for the collection of data only when incident beam  137  is on a target zone  135 . Optical bio-disc  130  includes a trigger mark  166  that is read by trigger sensor  141 , which feeds the trigger signal to capture trigger card  167 . Capture trigger card  167  is preferably, but not necessarily, implemented on buffer card  152 . Trigger sensor  141  may be located on the bottom side of disc assembly  130 . The system may also include a top detector  160  for detecting transmitted light  162 . This light could pass through a semi-reflective disc, or through an area where portions of the reflective layer of the disc have been removed. Further aspects of the types of discs suitable for use with the present invention are discussed below in further detail. 
       FIG. 13  shows a plan view of disc  130  with target zones  135  and trigger marks  166 . Hardware trigger mark  166  is preferably disposed at an outer periphery of the disc, and preferably is in a radial line with target zones  135 . 
     Capture trigger card  167  provides a signal indicating when trigger mark  166  has reached a predetermined position with respect to investigational features  136 . This signal is processed through ADC  150 , and into PC  158  to synchronize processing that takes place in PC  158  with the location of trigger mark  166 . For example, trigger mark  166  is placed just prior to a sector in bio-disc  130  containing investigational structures. When PC  158  detects trigger mark  166 , PC  158  waits a short predetermined time, and then begins processing the signal extracted from the HF signal as data indicative of the presence of an investigational feature. At the same time, when trigger mark  166  is detected by PC  158 , PC  158  sets a timer for a longer predetermined time after which PC  158  again processes the signal extracted from the HF signal as operation information used to operate the optical disc drive. 
       FIG. 14  is a block diagram showing the relationship of PC  158  with optical disc drive  140 . According to an embodiment of implementation II ( FIG. 9A ) of the present invention, additional drive functionality, including top detector  160 , trigger sensor  141 , and processing circuitry, is preferably located on a single printed circuit board (TAD)  82 . This functionality thus detects transmitted light and trigger marks, and then amplifies an analog data signal based on the detected transmitted light. These additions are preferably made so that no change is needed to existing optical disc drive electronics. Therefore, a conventional optical disc drive may be modified prior to initial shipment, or retrofitted with the additional functionality without the need to alter existing hardware. 
     According to another embodiment of the invention, and as an alternative to trigger mark  166 , the trigger signal  83  could be provided in the operational data, such that encoded information on the disc indicates the location of the investigational features. In yet another embodiment, the entire disc is read, but only the data following a predefined set of data is maintained. In this way, all of the data on the disc is initially read into memory, and the data preceding the software trigger is later discarded. Optionally, a second trigger mark can be provided. This second mark can be useful to distinguish from among multiple target zones, while enabling the user to look at a particular zone of interest. If multiple trigger marks, with corresponding trigger detectors, are used, then each trigger mark must be located at a different radius. 
     ADC  150  may also receive analog drive signals via buffer amplifier card  152 , which receives its input signals from optical drive  140 . Within PC  158 , CPU motherboard  87  communicates with optical disc drive  140  over a small computer systems interface (SCSI)  88  and receives data through an expansion bus from ADC  150 . CPU motherboard  87  has an Ethernet connection  88  that allows this data to be offloaded for further processing. A power supply  89  receives a power input and provides the power to CPU motherboard  87  as well as to the other components in the optical disc drive housing and in PC  158 . 
     The data can be processed as it is collected in a real-time manner, or may be stored and post processed by other computers, potentially reducing the complexity of the system. 
     The trigger, amplifier, detector card TAD  82  is preferably constructed in such a manner that it can be mounted within a conventional optical disc drive of the type that can be used in a drive bay in a computer. One suitable drive used particularly for development purposes is the Plextor model 8220 CD-R drive. While a CD or DVD can be used, a CD-R drive has several useful aspects. Because the CD-R drive allows reading and writing functions, the laser can operate over a higher range of power levels. This functionality of using higher power can be useful for certain types of investigational features. Another useful aspect of a CD-R is that it has the ability to write onto a disc and therefore can be used to write results back onto a disc. This allows results to be saved back onto the disc for later use and to remain with the disc. 
       FIG. 15  is a top view of TAD  82  including a triggering detection assembly according to another aspect of the present invention. The circuit board includes an opening or pass-through port  80  which is needed when implemented in a top detector drive arrangement utilizing a transmissive disc such as those disclosed in commonly assigned U.S. Pat. No. 5,892,577 entitled “Apparatus and Method for Carrying Out Analysis of Samples,” incorporated herein by reference, and U.S. Provisional Application No. 60/247,465 entitled “Disc Drive for Optical Bio-Disc.” When employed with conventional drives using reflective discs and a typically positioned proximal or bottom detector, the pass-through port  80  is not required. As discussed in conjunction with  FIG. 12 , the TAD  82  includes trigger sensor  141  and the detector  160 . In this particular embodiment, three detectors  160  are used. 
       FIG. 16  is an electrical schematic of the triggering circuit shown in  FIG. 15 . To acquire information concerning the investigational structures, the optical disc drive according to the present embodiment is provided with suitable triggering circuitry implemented to trigger when detection of the unprocessed HF signal  50  ( FIG. 4 ) is needed. This is necessary because the type of signal processing performed by DSP  32  ( FIG. 8 ), which typically includes demodulation, decoding, and error checking, is intended to convert EFM-encoded information on HF signal  50  to a specific digital format. Although the portion of the disc that provides operational information produces digital formatted data, the investigational features of the present invention do not produce EFM-encoded information. HF signals processed in a manner to decode EFM-encoded information cannot be easily used to detect the dual peaks associated with investigational structures. Thus, the signal or signals of interest are tapped-off before reaching the optical drive&#39;s DSP, and trigger mark  166  and trigger circuitry shown in  FIGS. 14 and 26  are implemented as discussed above. 
       FIG. 17  is a block diagram that illustrates in more detail the inter-relationship between TAD  82  and the disc drive mechanisms. As it is shown here, optical components  92  are mounted on a carriage assembly  172  that is driven by a carriage motor  94 , and the disc is driven by the disc motor  95 . The carriage assembly  172  includes an optical pick-up unit (OPU). Controllers  96 , which receive signals from CPU  87 , drive the two motors. Data from the optical components  92 , triggering detector signal  83 , and signals  83  from transmissive (top) detector  160  or detector array are all provided to TAD  82 . The detector for processing the signal from the transmitted or reflected beam of light may be a single detector element or an array of multiple elements arranged radially or circumferentially, and may be placed on the opposite side of the disc from the laser, and may be mounted directly on the TAD or separately. 
     ADC  150  may optionally be located on a sampling card that allows for very high-speed conversion. One usable card is the Ultrad AD 1280 DX, which has two 12-bit A/D converters sampling up to forty million samples per second. 
     There are advantages to making changes to the disc drive that provide the least amount of disruption to conventional drives. For this reason, it can be desirable to use a disc that is transmissive. In other words, the disc is reflective enough for the operational data to be seen by the active electronics and normal drive functioning to occur. Yet, still partially transmissive to allow some of the incident light to pass through the disc to a top detector. In this manner, the investigational features can be detected without it being necessary to alter the detection circuitry for reflected light. The reflected light may still be used to read encoded data. 
     Referring next to  FIG. 18 , TAD  82  illustrated by functional blocks can include transmissive or top detectors  160  located over the viewing regions or pass through port  80  as illustrated. This detector can be a single detector, an array arranged with different segments oriented radially, or an array with multiple segments oriented circumferentially with multiple detectors arranged along different radii. The detector unit  160  receives signals and provides them to a preamplifier  120 , automatic gain control  122 , switch  124 , and amplifier  126  to produce a signal on the order of 3 volts. 
     Triggering light source and detector  141  can be provided on TAD  82 . This hardware would include a light source and a detector positioned to detect trigger marks, preferably at the periphery of disc  130 . In this particular embodiment, a second trigger light source and detector  128  is provided to help distinguish from among a plurality of trigger marks. In this case, both trigger signals are provided to a trigger control circuit. The trigger control circuit passes trigger signals to collect and retain data from the desired sample areas on to ADC  150 . 
     Analog switch  124  can be used when the data detector is an array with multiple elements. There can be multiple detector elements that perform some of the types of refracted light combinations. For example, sums and differences can be used. If desirable, the switch can also be coupled to the detection elements that are under the disc for detecting reflected light. This could allow the system to obtain a differential between the top and bottom detection. 
     Additional processing and counting functionality can be provided on TAD  82  in order to remove the processing from ADC  150 , or to effectively replace ADC  150  and PC  158  ( FIG. 9A ) to allow more processing to occur on TAD  82 . In the case of the test for CD4/CD8, for example, one methodology that is used is to count white blood cells in a target region. Such methods are disclosed in commonly assigned U.S. patent application Ser. No. 09/988,728 entitled “Methods and Apparatus for Detecting and Quantifying Lymphocytes with Optical Biodiscs” filed Nov. 16, 2001. As the laser light is scanned over the assay region, the detector will detect no light at the edge of a blood cell, and will detect full light when centered on a blood cell. As the beam is scanned, it therefore creates a series of high and low signals indicating where a cell is detected. Processing functionality can be added to the card to include threshold crossing circuitry and a counter. Such processing is less complex than that which may be used for other tests. Each of these types of circuits is generally known. Depending on the type of test that is used (the CD4/CD8 being one example), the processing system may need to count hundreds or up to tens of thousands of features in the assay region or target zone. In addition, a microprocessor could also be added to the card. 
     By providing additional processing and/or counting functionality onto the card, the results from scanning the sample can be provided directly from the card via a USB port or through an Ethernet port. By using Ethernet, data can be provided from a web server so that users can access data with a web browser. 
     TAD  82  can also include a temperature sensor (not shown) as well as other sensors that may be useful for testing. In the case of temperature, a test may use relative temperature to indicate the presence of some material. Another detector that can be provided is a simple barcode reader that can be used if barcodes are provided on the disc for identification purposes. 
     The automatic gain control (AGC)  122  and automatic level control (not shown) make sure that the full dynamic range is used, and thus the signals may range, for example, from 0 to 3 volts. The automatic level control (ALC) is used to define a center of the signal, such as 1.5 volts if, for example, the range is 0 to 3 volts. The result of the amplification, ACG, and ALC is that the output can be processed through a threshold circuit and provide consistent results. 
     As a concrete example of the embodiments depicted in  FIGS. 9A and 12 , an inventive drive of the present invention includes a known optical disc drive that has been modified to include capture trigger card  164 , buffer  152  and ADC  150 . The inventive drive and a setup optical disc are sold, for example, to a research laboratory. The setup optical disc contains drive software and is of a known type of optical disc. The research laboratory connects the inventive drive to a known PC (e.g., PC  158 ) and runs the setup optical disc to install drive control software that enables PC  158  and the inventive drive to operate as a research instrument. Then, diverse types of optical bio-discs  130 , that include trigger mark  166  and target zones  135 , are sold to the research laboratory to enable diverse investigations and assays to be conducted. Bio-disc  130  may include target zones  135  and related microfluidics in one sector and encoded information in another. The encoded information includes operational information used to operate the optical disc drive and includes data about the type of tests that may be performed by the particular optical analysis disc. Different tests may require different discs and the encoded information on the disc then provides PC  158  with information about the particular test being run. 
       FIG. 19  is a top plan view of an optical disc drive assembly with the housing removed to show the disc tray  168 , the spindle  170 , the carriage assembly  172 , the optical head assembly  174 , and the ribbon cable  178 , which transmits signals to and from the optical head assembly. The carriage assembly  172  provides linear movement to optical head assembly  174  along rails  173 . Optical head assembly  174  contains lens assembly  176  for focal adjustments of incident and reflected light. 
       FIG. 20  is a bottom perspective view of the optical disc drive assembly of  FIG. 19 , illustrating the physical layout of the chip set, related electronic circuitry, and ribbon cable  178  from head assembly  174  ( FIG. 19 ) as unplugged from ribbon cable connector  179  on circuit board  177 . Signals transmitted to and from optical head assembly  174  may be acquired either directly from ribbon cable  178 , at the leads connecting ribbon cable connector  179  to circuit board  177 , or at particular solder points  180  on circuit board  177 . 
       FIG. 21  is a block diagram depicting interconnections between prior art optical disc reader  140  and buffer amplifier card  152  according to an embodiment of implementation  11  ( FIG. 9A ) of this invention. A chip set  30  ( FIG. 8 ) according to the present invention is shown to include taps from the A, B, C, and D outputs of detector  18 .  FIG. 21  further illustrates that the F−, F+, T−, T+, HF-AC coupled, and HF-DC coupled signals may also be tapped off of the HF matrix amplifier  18 A of optical disc drive  140 . These tapped signals provide access to raw, unprocessed analog signals produced by detector  18  and by the HF matrix amplifier  18 A. This permits external instrumentation to receive the signals without interfering with normal drive operation. Such external instrumentation may alternatively include the modified PC  142 , the audio processing module  156 , the external ADC  150 , or the external buffer amplifier card  152  and external ADC  150  as shown in  FIG. 9A . As indicated above,  FIG. 21  is directed to implementation  11  of the invention as generally illustrated in  FIG. 9A . 
       FIG. 22  is a top perspective view of one physical embodiment of the external buffer amplifier card  152  ( FIGS. 9A and 21 ) adapted to receive signals from optical head assembly  174  ( FIG. 19 ) and drive buffer  151  ( FIG. 12 ) according to the A to D embodiment of the present invention. This electrical device outputs and buffers the operational signals of an optical disc drive. Signals from optical head assembly  174  enter buffer amplifier card  152  at the pins of connector  155 . The signals are amplified and buffered via independent groups of resistors, capacitors, and op amps, then directed to output section  157 . This embodiment of buffer amplifier card  152  provides 9 to 11 output signals, including Quadrant A, Quadrant B, Quadrant C, Quadrant D, Detector E, Detector F, Un-Equalized HF, Equalized HF, AC coupled HF, Tracking servo response, and Focus servo response. 
       FIG. 23  is a perspective view of an alternative embodiment of external buffer amplifier card  152  illustrated in  FIG. 22 . The input signals from the optical head assembly enter at connector  155 . The signals directed to the optical disc drive&#39;s internal drive buffer  151  ( FIG. 12 ) exit through output section  157 , while processed signals are directed through connector  159  to external buffer amplifier card  152  ( FIG. 12 ). 
       FIG. 24  is a graphical representation illustrating the relationship between  FIGS. 24A ,  24 B, and  24 C.  FIGS. 24A ,  24 B and  24 C are electrical schematics of the amplifier stages according to a first embodiment of the buffer cards shown in  FIGS. 22 and 23 . 
       FIG. 24A  is a partial electrical schematic of the buffer amplifier. The analog HF signal  50  ( FIG. 4 ) from optical head assembly  174  ( FIG. 19 ) is taken from pins  1  and  2  of connector  155  ( FIGS. 22 and 23 ). The input signal travels across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a variable feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the HF 1  signal output at connector J 5  of output section  157  ( FIG. 22 ). 
     The analog F+ signal from optical head assembly  174  is taken from pins  3  and  4  of connector  155 . The input signal travels across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a fixed feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the FC+ signal. 
     The analog F− signal from optical head assembly  174  is taken from pins  5  and  6  of connector  155 . The input signal travels across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a fixed feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the FC− signal. 
     The analog T+ signal from optical head assembly  174  is taken from pins  7  and  8  of connector  155 . The input signal travels across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a fixed feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the TC+ signal. 
     The analog T− signal from optical head assembly  174  is taken from pins  9  and  10  of connector  155 . The input signal travels across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a fixed feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the TC− signal. 
       FIG. 24B  is another partial electrical schematic of the buffer amplifier. The analog HF-AC signal from optical head assembly  174  ( FIG. 19 ) is taken from pins  11  and  12  of connector  155  ( FIGS. 22 and 23 ). The input signal travels through an input load capacitor, then across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a variable feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the HF-AC signal output at connector J 3  of output section  157  ( FIG. 22 ). 
     The analog HF-A signal from optical head assembly  174  is taken from pins  19  and  14  of connector  155 . The input signal travels across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a fixed feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the HF-A signal output at connector J 8  of output section  157 . The signal is also tapped at the output lead prior to the stabilization capacitor to feed an HF-A signal into the A to D circuit of the HF 2 (DC) output at connector J 7  ( FIG. 24C ). 
     The analog HF-B signal from optical head assembly  174  is taken from pins  17  and  16  of connector  155 . The input signal travels across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a fixed feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the HF-B signal output at connector J 9  of output section  157  ( FIG. 22 ). The signal is also tapped at the output lead prior to the stabilization capacitor to feed an HF-B signal into the A to D circuit of the HF 2 (DC) output at connector J 7  (See  FIG. 24C ). 
     The analog HF-C signal from optical head assembly  174  is taken from pins  15  and  18  of connector  155 . The input signal travels across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a fixed feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the HF-C signal output at connector J 10  of output section  157  ( FIG. 22 ). The signal is also tapped at the output lead prior to the stabilization capacitor to feed an HF-C signal into the A to D circuit of the HF2(DC) output at connector J 7  (See  FIG. 24C ). 
     The analog HF-D signal from optical head assembly  174  is taken from pins  13  and  20  of connector  155 . The input signal travels across an input load resistor and a voltage stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a fixed feedback loop. The amplified signal is directed across an output load resistor and stabilization capacitor before becoming the HF-D signal output at connector J 11  of output section  157  ( FIG. 22 ). The signal is also tapped at the output lead prior to the stabilization capacitor to feed an HF-D signal into the A to D circuit of the HF 2 (DC) output at connector J 7  (See  FIG. 24C ). 
       FIG. 24C  is yet another partial electrical schematic of the buffer amplifier. The FC+ and FC− signals from  FIG. 24A  are directed through independent input resistors and then combined. The combined signal is fed into the negative input of an op amp, with a variable positive voltage feeding the positive input. The amplified signal is buffered with a fixed feedback loop and directed through a variable resistor into the negative input of a second op amp. The amplified signal from the second op amp is buffered with a second fixed feedback loop and directed across an output resistor and stabilization capacitor before becoming the FOCUS output at connector J 2  of output section  157  ( FIG. 22 ). 
     The TC+ and TC− signals from  FIG. 24A  are directed through independent input resistors and then combined. The combined signal is fed into the negative input of an op amp, with a variable positive voltage feeding the positive input. The amplified signal is buffered with a fixed feedback loop and directed through a variable resistor into the negative input of a second op amp. The amplified signal from the second op amp is buffered with a second fixed feedback loop and directed across an output resistor and stabilization capacitor before becoming the TRACKING output at connector J 6  of output section  157  ( FIG. 22 ). 
     The tapped HF-A, HF-B, HF-C, and HF-D signals from  FIG. 24B  are individually directed through input resistors and then combined as illustrated. The combined signal is fed into the negative input of an op amp, with a variable positive voltage feeding the positive input. The amplified signal is buffered with a fixed feedback loop and directed through a variable resistor into the negative input of a second op amp. The amplified signal from the second op amp is buffered with a second fixed feedback loop and directed across an output resistor and stabilization capacitor before becoming the HF 2 (DC) output at connector J 7  of output section  157  ( FIG. 22 ). 
     Modifying an Optical Disc Drive—Software 
     In accordance with other principles of the present invention, it is possible to programmably reconfigure chip set  30  ( FIG. 8 ) so that physical modification of the optical disc drive is not necessary. One way this may be accomplished is by programming DSP  32  ( FIG.8 ) to operate simply as an A/D converter rather than as, inter alia, a demodulator/decoder. In such a configuration, the DSP chip takes the place of external ADC  150  and supplies the digitized HF signals directly to a host data bus. Investigational structures may be detected by analyzing the resulting digitized HF signal. Alternatively, investigational structures could be detected by routing an unprocessed HF signal through the chip set  30  to an output terminal of optical disc drive  140  ( FIG. 9A ), connecting the signal to a personal computer (e.g., PC  158 ), and using hardware and/or software within the personal computer to perform the A/D conversion. 
     It is possible to programmably configure DSP  32  as an A/D converter without additional demodulation and error correction in multiple ways. For example, a configuration routine stored in program memory  39  ( FIG. 8 ) may operate via controller  38  ( FIG. 8 ) to reconfigure DSP  32 . Alternatively, an application program may be able to selectively reconfigure DSP  32  through interface circuitry  36  ( FIG. 8 ) as required. DSP  32  may also configure itself as an A/D converter when it receives a certain type of HF signal. These methods are merely illustrative, and any other suitable software or firmware based reconfiguration methods or path may be used if desired. 
       FIG. 25  is a functional block diagram of a digital signal processing circuit programmably configured as an analog-to-digital converter in accordance with the principles of an embodiment of implementation III the present invention as represented in  FIG. 9A .  FIG. 25  illustrates some of the ways in which the processing resources within DSP  32  may be reconfigured to produce a suitable A/D converter according to the present invention. In one possible arrangement, for example, A/D block  42  may be disconnected from path  45  and connected directly to output interface  48  through path  43 . In this case, the digitized HF signals completely bypass blocks  44  and  46  and travel to output interface  48 . In another arrangement, digitized signals from A/D block  42  travel on path  45 , but pass through blocks  44  and  46  without being processed. In some embodiments, it may be desirable to temporarily discontinue power supply to blocks  44  and  46  or place them in a low-power operating mode to reduce power consumption (e.g., in battery operated disc drives). Although the foregoing illustrates several possible A/D converter arrangements, any other suitable arrangement of resources within DSP  32  may be used if desired. 
     If the bypassing of unneeded functionality can be accomplished through programming, no change to existing hardware is needed, although a modification may be needed to drive firmware. 
       FIG. 26  is a flow chart illustrating some of the steps involved in detecting investigational elements in accordance with the DSP embodiment of the present invention illustrated in  FIG. 25 . As shown in  FIG. 26 , when it is desired to enter detection mode (step  100 ), a portion of a signal processing system within the drive is configured to operate as an analog-to-digital converter (step  101 ). This may include programmably reconfiguring one or more chips in chip set  30  (e.g., DSP  32 ) by employing a remote application program or by using a routine stored in a local program memory  39 ,  FIG. 6 . This conversion eliminates the need to physically modify the disc drive electronics, and it allows the invention to take advantage of the configurable processing resources within chip set  30 . 
     At step  102 , a plurality of analog data signals are acquired from disc  130  ( FIG. 12 ), which preferably includes investigational structures  136  ( FIG. 12 ), using objective assembly  10  ( FIG. 1 ). Next, at step  103  the analog data signals are combined to produce a sum (HF) signal  50  ( FIG. 4 ) and a tracking error (TE) signal  52  ( FIG. 4 ). Both signals are provided to the signal processing system at step  104 . At step  105 , the basic information required to operate the disc drive (such as tracking, focus, and speed control) is extracted from TE signal  52 . Simultaneously, the signal processing system converts the HF signal  50  into a digitized signal, which is provided to output interface  36  ( FIG. 8 ) at step  105 . The digitized sum signal is subsequently used to characterize the investigational features or structures  136  present on disc  130 . Once the scanning process is complete, disc drive  140  may be directed to exit the detection mode (step  106 ). At this point, the portion of chip set  30  (e.g., DSP  32 ) previously configured as an A/D converter may be returned to its original configuration and normal CD, CD-R, or DVD operation may resume (step  107 ). 
     In a variant of the trigger mark  166  ( FIG. 13 ) and trigger circuit  167  arrangement, a registration mark on optical disc assembly  130  itself may be encoded and recorded. Certain digital binary autocorrelation codes (i.e., a sequence of binary bits) may be used to encode the registration mark. For example, the known Barker code is a series of bits (varying in number up to thirteen bits) that has a sharp autocorrelation function with a peak equal to the number of bits (when registered or correlated) and side lobes (when not registered or correlated) equal to one. See Barker, R. H., “Group Synchronization of Binary Digital Systems,” as it appears in Jackson, W. (ed.),  Communications Theory,  Academic Press, New York, 1953, pp. 273–287, incorporated herein by reference. 
     In a concrete example, one thirteen bit Barker code is known to be 1111100110101. When a digital bit stream containing this 13 bit long code is correlated with a receiver searching for this 13 bit long code as a reference, a perfect registration will produce a correlation with 13 identical bits. However, if the bit stream were to be slid forward or back by up to 12 bits, the peak correlation side lobe would be only 1 bit. 
     Other autocorrelation functions are known with low side lobe out of correlation values and high in correlation values. See Lindner, J., “Binary Sequences Up To Length 40 With Best Possible Autocorrelation Function,”  Electron. Letters,  vol. 11, p. 507, October 1975. For example, there are two known codes of length 25 bits, one of which, expressed in octal, is 163402511. An octal digit varies from 0 to 7 and represents, in order, binary 000, 001, 010, 011, 100, 101, 110, and 111. This code has a maximum peak side lobe of 2 and a correlation peak of 25. There are 114 known codes of length 40, one of which, expressed in octal, is 14727057244044. This code has a maximum peak side lobe of 3 and a correlation peak of 40. 
     Long autocorrelation codes are also characterized by low correlation values with random bits received in a sequence, and high correlation values when the exact code is detected and registered in the bit stream. A bit stream recorded on an optical disc assembly might be constructed to include an autocorrelation code within the data bit stream. A signal processor that analyzes the bit stream would then correlate the bit stream with the autocorrelation code being sought within the incoming bit stream. When the correlation processor encounters the autocorrelation code in the bit stream, the correlation function spikes up very high in relation to normal correlation values with random bit stream data. This provides a registration mark in the same sense that trigger mark  166  provides a registration mark. 
     Referring again to  FIG. 12 , optical disc assembly  130  is divided into a sector with investigational features or signal elements  136  situated within target zones  135  and a sector  133  containing operational information used to operate the optical disc system. In this variant, the operational information advantageously includes data, at least some of which includes an autocorrelation code. This data is stored on a sector of optical disc assembly  130  in known ways (e.g., CD ROM, DVD, etc.). When the autocorrelation code is detected and registered in the data stream from the optical disc assembly, two timers are set in PC  158  (or equivalent circuitry). The beginning of the sector containing the investigational features is marked by an expiration of the first timer, and the ending of the sector containing the investigational features is marked by an expiration of the second timer. The duration of the two timers is advantageously included in the data stored on optical disc assembly  130  so that a common disc drive system can be used for different types of bio-discs with different size sectors in which the investigational features are stored. 
     A conventional optical disc reader generally allows a user to play a disc, while giving the user little ability to control the parameters of the reading, rotating, and data processing. For the most part, users of commercial CD and DVD players would not need such abilities. These firmware-based modifications can generally be made using aftermarket software. In other words, the programming could be provided on a disc or could be available by download via the Internet. 
     Another modification to the conventional CD reader is a technique shown on  FIG. 86 . Channel bit generator  1000  is used to generate known good data bits and then add them to the data bits actually received from the read out of an optical disc containing ho-bits, as represented by pick up  1002 . The sum of bits is then sent to block decoder  1004  where block error information can be obtained. 
     Additional modifications suitable for use in the invention include, but are not limited to, one or more of the following capabilities: 
     1. Wobble groove playback and random access on a wobble groove, rather than needing to start from the beginning of a disc. This allows the drive to go to an LBA (or an address by some other mode) and play forward from there. 
     2. Poll the laser monitor value, which allows reading of the value of the laser power detected by the laser power monitor detector in the optical pickup unit. 
     3. Poll and set the laser power read/play value, which allows a user to monitor and set the power command value to the laser. 
     4. Poll the automatic gain control (AGC) to get the value of the AGC. The gain is controlled to make sure that the detected signals have consistent amplitude. The amount of gain therefore is an inverse indicator of the signal intensity. Consequently, the signal can be used for detection and measurement. 
     5. Poll the tracking automatic gain control value. 
     6. Monitor the C1 and/or P1 decoder activity at a port to monitor types of errors and attain error counts. This is useful because the errors could be useful information for detecting the location of an investigational feature. A conventional drive detects gaps in the encoded data as an error. 
     7. Monitor the C2 and/or PO decoder activity at a port. See No. 6 above. 
     8. Initialize and track operational features on an analysis disc independent of encoded logic. This refers to the ability to control the laser position and control the speed of the disc independent of the data. This functionality allows a user to send a command to keep the drive motor spinning without its operational functions of focus, tracking, and synchronization. 
     9. Initialize the drive with a specific speed and laser read power. A drive typically has a fixed start-up speed and laser power. This change allows these values to be set and changed by the user. In a typical disc drive system, however, the disc immediately starts to spin to get a focal point, get synchronization information, and find a table of contents. If the information is not found, the disc drive will open up and shut down. In certain circumstances, it may be desirable not to spin the disc as soon as it is inserted into the disc drive. For example, it may be desirable to prevent the drive from automatically spinning when a liquid sample is added to the disc. This change also relates to the change set out in No. 15 below. 
     10. Stream the main and sub-channel data in all areas of the disc including lead-in and lead-out, which allows more portions of the disc to have data. 
     11. Push raw-EFM (eight-fourteen modulation) value to a port or secondary port, which allows the user to see 14-bit data before it is translated to 8-bit values. This functionality enables the user to more clearly know exactly what is on the disc. Like No. 10 above, this change allows additional areas on the disc to be used. 
     12. Push buffered, DC coupled signals, such as TE, FE, and HF, to an external port. This relates to the ability to provide these signals to an external port for additional processing, whereas they are generally used for internal purposes (see  FIGS. 4 and 8 ). 
     13. Decode and poll values collected from the power calibration area (PCA) and program memory area (PMA) at initialization. This allows additional information to be collected. 
     14. Pause playback of a disc and open the tracking servo to monitor the open loop tracking signal, which allows the user to monitor the eccentricity of the disc. A disc generally has some eccentricity and therefore, the tracking signal will have a periodic form as the disc is rotated. The eccentricity of the disc arises from imperfect processing of the disc. The tracking signal is thus a reflection of the eccentricity that produces a periodic signal, which is a reflection of the eccentricity. If there is a change in reflectivity in one area, such as due to the presence of an investigational feature, the tracking signal will reflect this change in reflectivity. 
     15. Set Ghost initialization logic. As indicated in No. 9 above, when a disc is put into a disc drive, it typically starts spinning. One of the initial functions is to find a table of contents. Accordingly, this change allows the user to provide a table of contents to the disc drive controller effectively tricking the disc drive into thinking that it has read the table of contents from the disc. 
     16. Interactively turn off tracking function. 
     17. Control and monitor the focusing offset with or without the tracking function. The focus offset changes the size of the laser spot, and thereby changes the amount of energy incident upon the disc. In certain circumstances, it may be desirable to provide heat to the disc or a region of the disc for optimal assay conditions. Therefore, the ability to control the focus offset can allow the user to control heat distribution. 
     18. Switch layers on a DVD. 
     19. Monitor value changes at the switching port. 
     20. Read a CD or CD-RW with a DVD laser. The DVD laser is at a lower wavelength, which can be useful for imaging and for fluorescent detection. Devices that have the ability to read CD and DVD are generally provided with two lasers, one for each mode. 
     21. Track a wobble groove (1.2 mm) at any frequency with a DVD laser. 
     22. Monitor the value of a buffered differential phase detection (DPD) signal. The DPD signal is a DVD signal used for tracking, and thus corresponds to the previously discussed ability to monitor the tracking signal. 
     23. The use of a near field optical assembly to detect structures that violate the diffraction limitations of the laser diode. 
     24. Utilize the servo to detect defect or structure. Servo will push signal one way when the defect or structure is about the surface. The servo will go another way when the defect or structure is below the surface. 
     25. The use of phase delay detection in a DPD optical assembly to detect the presence of structures on an optical disc. 
     26. The use of DPD focus servo electronics to detect the presence of structures that generate digital biology components. 
     27. Creation of a second surface mastering system that utilized wobble tracking. A DVD RAM drive is used as a base unit and a DVD master is created using wobble groove tracking. The pits are formed from Ablation. 
     28. The use of a secondary focus place and a second laser to isolate the tracking system from the biobit detection plane and system. This design will be effected by the characteristics of the distribution of the biobit spheres. 
     Using EEPROM to Upgrade Existing Optical Drive 
     Some of the software modification described in the previous section can be made via a software upgrade to the Electrically Erasable Programming Read Only Memory (EEPROM) in existing optical drive. When utilizing a consumer optical disc reader it is possible to upgrade or configure the operation of the reader by uploading a program to an EEPROM in the optical disc circuitry. The program will replace or append the information that is in position on the EEPROM. The program is written to optimize the operation of the drive for the measurement of biological substance or biobits. The program will also change the aspects of the information that is used to communicate with the drive. The program will also change the information that is collected from the drive during or after measurement or detection operation. 
     The program may be contained on the optical disc in a bootable (EL Torito Specification) format. A byte is placed in a known position or sector (CD or DVD sector) that tells a qualified operating system (bootable BIOS or firmware) to utilize the information on the disc as an Operating System. This capability is common to most BIOS or other I/O systems in the market place (i.e. Adaptec, Award, Phoenix, etc.). In effect, the identified byte will tell the computing device to reload the operating system that is contained on the disc. The operating system will then run a loading program that is contained on the disc. 
     The loading program is written to manufacturer specifications in format. The loading program is written to application specifications in content. The loading program is moved into the EEPROM in the circuitry of the drive by using the communication protocol of the port. These protocols include the byte commands outlined in the industry specification for ATAPI 1 &amp; 2 (Small Form Factor Committee 80201–80901) and SCSI device formats for SCSI 1, 2 and 3 (ISO Standards). The physical outline of communication for SCSI and ATAPI devices are physically different. Some manufacturers are allowed to use a proprietary byte communication format that is not covered in the standard. The present invention may utilize these proprietary specifications. The Chipsets that are utilized by the drive manufacturers also have some protocols that will be documented in the program form and the program content. 
     The information that is gathered from the drive during operation is gathered from the drive through the port (SCSI or ATAPI) and is interpreted by a software program called a driver. The driver may be a proprietary driver contained in part by the operating system (e.g. Microsoft Windows™) or in part by the manufacturer of the drive. The driver may also be contained in part by the manufacturer of the chipset that is used to operate the communication port electrically. The driver may also be replaced or amended by a program that is application specific and is loaded into the operating system by the loading program on the disc. 
     The data that is gathered from the adjusted drive is gathered from the physical port and interpreted by the driver. The data that is collected is also outlined in form by the Specifications for communication with ATAPI and SCSI devices. The data may also be collected through a proprietary format that is loaded on the drive. This proprietary format may include adjusted chipset communication protocol, adjusted port communication protocol or an adjusted or non-standard driver. 
     The specific data area involves collection of data from the operation of the Reed-Soloman decoder of the optical disc reader. This includes the C1 and C2 activity of the CIRC (Cross Interleaved Reed Soloman) code of an optical disc playback unit, the inner and outer parity activity of the RSPC (Reed-Soloman Product) code of a DVD playback unit, or the CCRC/CRC (Cyclic Redundancy Check Code) information from any block or sector structure contained in an optical disc format. The data is provided to the port or the driver in packet format and is relevant to the biological measurements that the present invention is designed to make. 
     DVD Technology 
     The use of DVD technology provides a dramatic increase in the operational margin that is offered by the lower wavelength in the laser diode, and by the drastic increase in density and operational information that is included in the disc format. The bio-bits or signal elements including beads, cells, colloidal gold, carbon, or other microscopic markers and reporters associated with an optical disc, can be located on layer  0  or layer  1  of a DVD disc assembly. Disc designs relating to this aspect of the present invention are more fully described in commonly assigned co-pending U.S. patent application Ser. No. 10/006,620 entitled “Multiple Data Layer Optical Discs for Detecting Analytes”, filed Dec. 10, 2001, which is herein incorporated by reference. 
     Layer  0  of a DVD disc is manufactured as a second surface disc. This disc can be manufactured with very little information at the inner diameter so that it will not interfere optically with the detection of bio-bits on the outer diameter of layer  1 . Layer  0  may be utilized as an adaptable optical spacer that is placed on layer  1  after processing a bio-bit application. Layer  1  is manufactured as a first surface layer. Normally, it is glued onto layer  0  with special glue that has similar refractive properties to the molded plastic layers (e.g., between 1.54 and 1.58). This maintains optical efficiency and very little loss of signal in the reflected or return path. The specified thickness of this layer is 40–60 microns. The transmissive properties of the outer layer, or layer  0 , are preferably then designed to make up for a significant loss of signal resulting from a tiny air interface. 
     The DVD system is designed to provide automatic signal gain and recover information from surfaces with a reflectivity as low as 30% (only defined for dual layer formats). Automated tilt control may be necessary for this method. The use of multiple lasers will be utilized in this technological application. Layer  0  may become an operational layer that will contain information to provide for the operational requirements of the system. A second layer will be used on layer  1  that will detect the bio-bits, signal elements, or investigational features. Layer  1  may or may not contain pits, lands, or grooves. In one particular embodiment, the bio-bits, signal elements, or investigational features are applied to a DVD-R, DVD-RW, or DVD-RAM application with zoned clocking or pitted wobble groove applications. A “hybrid” disc in a DVD system is employed as a stepping-stone for this bio-bit detection technique. The word “hybrid” entails the use of multiple densities. For example, layer  0  is of DVD density and layer  1  is of CD density. 
     The idea is to create a hybrid sick such as the one shown in  FIGS. 87A and 87B .  FIG. 87A  is a side view of the hybrid disc and  FIG. 87B  is a top view of the disc. An 8 cm CD is manufactured and adhered to the center of a single laser DVD-RAM or DVD-RW disk. The CD portion would basically represent later  1  of a DVD disk and include information related to performing the bio assay, such as programs for the drive electronics, disk speed, etc. As shown in  FIG. 87A , layer  1   1008  (8 cm CD layer) is on top of layer  0   1006 . Underneath layer  0  ( 1006 ) is substrate layer  1016 . At the end of a CD portion, the drive is instructed to skip to layer  0   1006  and being reading the outer portion of the disk. The structures to be measured are located in the recess  1014  on the underside of the cover  1012 . Several recesses are distributed across the different sectors of the disc, in the outer portion of layer  0  ( 1006 ), as shown in  FIG. 87B . In an alternate embodiment, capillary tubes could be used instead of a recess. Since the space between layers L 0  and L 1  is in the order of 40 um, there is room for potentially large biological structures. 
     With this embodiment, the cover contains the bio-assay and is replaced for each assay performed. The remainder of the disk could be reused for further assays provided it could be cleaned to prevent cross contamination. 
     One development in DVD technology enables a DVD drive to temporarily reprogram itself from information contained on a disk being read. This would provide a means for reprograming DVD drive electronics to perform any special processing required to detect the presence of the bio-bits, and to characterize any such bio-bits detected. For example, the bio-bits could be deposited in specific patterns on the disk. The disk would also include program code for detecting the presence of absence of the patterns and thereby detect the bio-bits. This would involve developing a code such as an RLL(2,10) code and programming the DVD electronics accordingly. 
     One difference in implementation in the DVD technology for the detection of biobits involves the use of wobble signal. There are significant differences between the wobble signal utilized in the CD recordable system and the DVD system. In the CD recordable system the present invention utilizes the wobble signal to provide a tracking signal that can be compared to a reference pulse to maintain speed control. The secondary wobble signal is very interesting. It utilizes a bi-phase mark encoding technique and provides several other pieces of information. The bi-phase mark method is a digital modulation method. This digital waveform is superimposed on the wobble signal and a bi-phase decoder is included in the CD Recordable unit to decode the information. The digital information that is encoded in the wobble signal includes logical position, power control information and specialized use information. The manufacturing technique for bi-phase mark and wobble signal is very unique. Mastering a CD recordable master requires a very specialized mastering system. The mastering” system uses 2 mastering lasers. One laser is utilized to make the wobbled groove and a secondary laser is modulated to create the bi-phase mark information in the wobbled signal. 
     In the DVD recordable system, the components used that are very similar to the components described above. The technology on the mastering level is somewhat similar in technique. The frequency (locking) utilized in this specification is 140 kHz or 7.143 microseconds. At a rotational velocity of 3.49 meters/sec the physical component of one wobble pattern would equal approx. ˜25 microns. This is still larger than most of the biological components that the present invention intends to measure. 
     Of greater concern is the design of the DVD rewritable standards. This standard utilizes a tracking and synchronization technique referred to as the wobbled land and groove format. The wobble signal frequency is increase to 160 kHz or 6.25 microseconds. At a speed of 3.49 meters/sec, the physical component can be measured is about 21.8 microns. 
     In the DVD rewritable standard the address information that was provided by the bi-phase mark patterns in the CD Recordable standard is no longer digitally modulated on top of the wobble signal. Embossed pit structures are placed at specific locations around the disc. These “Zones” contain the address information and some clocking information. This recording scheme is referred to as the ZCLV or Zoned Constant Linear Velocity technique. The areas between these “zones” contain a groove and a wobble signal. A unique feature that is utilized in the DVD-RAM technique is the land/groove switch tracking. In this technique we switch from land on one rotation to groove on the next. This is highly unusual but provides a high level of control. The lands have embossed pit structures for control applications and the groove contains the area for phase change recording. 
     In the present invention, the ability to decode the bi-phase mark information is limited the biobit pattern density is increased. These zones provides the exact areas for the detection of biobit patterns. This technique uses space on the optical disc but the tradeoff is a significant gain in the amount of positional accuracy. 
     Increasing Resolution 
     The power-monitoring signal in a CD or DVD recording system provides a response similar to that of a spectrophotometer. The power control signal or monitor signal of a recording laser diode can be controlled through logical information on the disc or through software. It may also include an analysis of the monitor signal as the focused incident beam is moved across an area of the disc. 
     An alternative embodiment measures the birefringent properties of an area on an optical disc. This would involve a modified player with a second additional optical path that is currently not available in the consumer market. This optical path involves the use of prisms instead of a rotating polarimeter. 
     In the areas of mathematics that are used in the decoding processor of a player, the lookup table (that is used to perform modulation or the movement of information from the data bits to the channel bits) can be replaced with a table to optimize detection of bio-bits, signal elements, or investigational features. The mathematics that is adjusted to run length (RLL 2,10) in the Reed Soloman encoding and decoding scheme can be optimized for detection of bio-bits. These adjustments provide information that is used for detection or statistical evaluation of bio-bits. The information is available using standard software detection of C1 or C2 errors on CD decoder interfaces. The information is also available utilizing standard software detection of PI or PO errors on DVD decoder interfaces. The PI/PO data from the DVD decoder may be used to characterize the sizes of bio-bits, signal elements, and investigational features. In one particular embodiment, the EFM or ESM patterns generated by the lookup table are replaced with simple 8-bit patterns that characterize the run length of the item under study. Changes to the decoding system of a player may be performed through a program that is contained in the information stored on the optical disc. The information is loaded into “Flash” EPROM or similar technology. 
     Another alternative embodiment uses a Solid Immersion Lens (SIL) in the detection of bio-bit technology. A SIL player increases operational resolution significantly. 
     Yet another alternate embodiment uses a CD-Recordable player that is optimized to read microscopic structures on the surface of an optical disc. The player is adjusted optically to detect the structures in the air interface on the surface of an optical disc. The disc is designed to utilize the CD-Recordable system to provide a platform for quantifiable measurement of microscopic structures. 
     Optical Bio-Discs 
       FIG. 27  is an exploded perspective view of the principle structural elements of one embodiment of a particular optical bio-disc  410 .  FIG. 27  is an example of a reflective zone optical bio-disc  410  (hereinafter “reflective disc”) that may be used in the present invention. The principle structural elements include a cap portion  416 , an adhesive member  418 , and a substrate  420 . Cap portion  416  includes an inlet port  422  and a vent port  424 . Cap portion  416  may be formed from polycarbonate and is preferably coated with a reflective surface  446  (see  FIG. 29 ) on the bottom thereof as viewed from the perspective of  FIG. 27 . In the preferred embodiment, trigger marks  166  ( FIG. 12 ) are included on the surface of the reflective layer  442  (see  FIG. 29 ). Trigger marks  166  may include a clear window in all three layers of the bio-disc, an opaque area, or a reflective or semi-reflective area encoded with information that sends data to a processor (e.g., ADC  150  as shown in  FIG. 12 ), that in turn interacts with the operative functions of the interrogation or incident beam  137  ( FIG. 12 ). The second element shown in  FIG. 27  is adhesive or channel layer member  418  having fluidic circuits  428  or U-channels formed therein. The fluidic circuits  428  are formed by stamping or cutting the membrane to remove plastic film and form the shapes as indicated. Each of the fluidic circuits  428  may include a flow channel  430  and a return channel  432 . Some of the fluidic circuits  428  illustrated in  FIG. 27  include a mixing chamber  434 . Two different types of mixing chambers  434  are illustrated. The first is a symmetric mixing chamber  436  that is symmetrically formed relative to the flow channel  430 . The second is an off-set mixing chamber  438 . The off-set mixing chamber  438  is formed to one side of the flow channel  430  as indicated. The third element illustrated in  FIG. 27  is substrate  420  including target or capture zones  135 . Substrate  420  is preferably made of polycarbonate and has a reflective layer  442  deposited on the top thereof (see  FIG. 29 ). Target zones  135  are formed by removing reflective layer  442  in the indicated shape or alternatively in any desired shape. Alternatively, target zones  135  may be formed by a masking technique that includes masking the target zone  135  areas before applying the reflective layer  442 . Reflective layer  442  may be formed from a metal such as aluminum or gold. 
       FIG. 28  is a top plan view of the optical bio-disc  410  illustrated in  FIG. 27  with the reflective layer  442  on the cap portion  416  shown as transparent to reveal the fluidic circuits  428 , the target zones  135 , the inlet ports  422 , the vent ports  424 , and trigger marks  166  situated within the disc. 
     With reference next to  FIG. 29 , there is shown an enlarged perspective view of the reflective zone type optical bio-disc  410  according to one embodiment of the present invention. This view includes a portion of the various layers thereof, cut away to illustrate a partial sectional view of each principle, layer, substrate, coating, or membrane.  FIG. 29  shows the substrate  420  that is coated with the reflective layer  442 . An active layer  444  is applied over reflective layer  442 . In a preferred embodiment, the active layer  444  may be formed from polystyrene. Alternatively, polycarbonate, gold, activated glass, modified glass, or modified polystyrene such as polystyrene-co-maleic anhydride, may be used. In addition hydrogels can be used. Alternatively, as illustrated in this embodiment, adhesive layer  418  is applied over active layer  444 . The exposed section of the adhesive layer  418  illustrates the cut out or stamped U-shaped form that creates the fluidic circuits  428 . The final principle structural layer in this reflective zone embodiment of the present bio-disc is cap portion  416 . Cap portion  416  includes the reflective surface  446  on the bottom thereof. Reflective surface  446  may be made from a metal such as aluminum or gold. Use of the type of disc illustrated in  FIG. 29  with genetic assays is disclosed in commonly assigned co-pending U.S. patent application Ser. No. 10/035,836 entitled “Surface Assembly for Immobilizing DNA Capture Probes and Bead-Based Assay Including Optical Bio-Discs and Methods Relating Thereto” filed Dec. 21, 2001, which is herein incorporated by reference. 
     Referring now to  FIG. 30 , there is shown an exploded perspective view of the principle structural elements of a transmissive type of optical bio-disc  410  according to the present invention. The principle structural elements of the transmissive type of optical bio-disc  410  similarly include cap portion  416 , adhesive layer  418 , and substrate  420 . Cap portion  416  includes inlet ports  422  and vent ports  424 . Cap portion  416  may be formed from a polycarbonate layer. Optional trigger marks  166  may be included on the surface of a thin semi-reflective layer  443 , as best illustrated in  FIG. 33 . Trigger marks  166  may include a clear window in all three layers of the bio-disc, an opaque area, or a reflective or semi-reflective area encoded with information that sends data to a processor (e.g., ADC  150  as shown in  FIG. 12 ), which in turn interacts with the operative functions of interrogation beam  137  ( FIG. 12 ). 
     The second element shown in  FIG. 30  is an adhesive or channel layer member  418  having fluidic circuits  428  or U-channels formed therein. The fluidic circuits  428  are formed by stamping or cutting the membrane to remove plastic film and form the shapes as indicated. Each of the fluidic circuits  428  may include flow channel  430  and return channel  432 . Some of fluidic circuits  428  illustrated in  FIG. 30  include mixing chamber  434 . Two different types of mixing chambers  434  are illustrated. The first is the symmetric mixing chamber  436  that is symmetrically formed relative to flow channel  430 . The second is the off-set mixing chamber  438 . Off-set mixing chamber  438  is formed to one side of flow channel  430  as indicated. 
     The third element illustrated in  FIG. 30  is substrate  420 , which may include target or capture zones  135 . Substrate  420  is preferably made of polycarbonate and has the thin semi-reflective layer  443  (shown in  FIG. 34 ) deposited on the top thereof. Semi-reflective layer  443  associated with substrate  420  of disc  410  illustrated in  FIGS. 31 and 34  is significantly thinner than the reflective layer  442  on substrate  420  of the reflective disc  410  illustrated in  FIGS. 27 ,  28  and  29 . Thinner semi-reflective layer  443  allows for some transmission of interrogation beam  137  through the structural layers of the transmissive disc as shown in  FIG. 12 . Thin semi-reflective layer  443  may be formed from a metal such as aluminum or gold. 
       FIG. 31  is an enlarged perspective view of substrate  420  and semi-reflective layer  443  of the transmissive embodiment of optical bio-disc  410  illustrated in  FIG. 30 . In a preferred embodiment, thin semi-reflective layer  443  of the transmissive disc illustrated in  FIGS. 30 ,  33 , and  34  is approximately 100–300 Å thick and does not exceed 400 Å. This thinner semi-reflective layer  443  allows a portion of incident or interrogation beam  137  ( FIG. 12 ) to penetrate and pass through the semi-reflective layer  443  to be detected by a top detector  160  ( FIG. 12 ) while some of the light is reflected or returned back along the incident path. As indicated below, Table 2 presents the reflective and transmissive characteristics of a gold film relative to the thickness of the film. The gold film layer is fully reflective at a thickness greater than 800 Å. While the threshold density for transmission of light through the gold film is approximately 400 Å. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Au film Reflection and Transmission (Absolute Values) 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Thickness 
                 Thickness 
                   
                   
               
               
                   
                 (Angstroms) 
                 (nm) 
                 Reflectance 
                 Transmittance 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 0 
                 0 
                 0.0505 
                 0.9495 
               
               
                   
                 50 
                 5 
                 0.1683 
                 0.7709 
               
               
                   
                 100 
                 10 
                 0.3981 
                 0.5169 
               
               
                   
                 150 
                 15 
                 0.5873 
                 0.3264 
               
               
                   
                 200 
                 20 
                 0.7142 
                 0.2057 
               
               
                   
                 250 
                 25 
                 0.7959 
                 0.1314 
               
               
                   
                 300 
                 30 
                 0.8488 
                 0.0851 
               
               
                   
                 350 
                 35 
                 0.8836 
                 0.0557 
               
               
                   
                 400 
                 40 
                 0.9067 
                 0.0368 
               
               
                   
                 450 
                 45 
                 0.9222 
                 0.0244 
               
               
                   
                 500 
                 50 
                 0.9328 
                 0.0163 
               
               
                   
                 550 
                 55 
                 0.9399 
                 0.0109 
               
               
                   
                 600 
                 60 
                 0.9448 
                 0.0073 
               
               
                   
                 650 
                 65 
                 0.9482 
                 0.0049 
               
               
                   
                 700 
                 70 
                 0.9505 
                 0.0033 
               
               
                   
                 750 
                 75 
                 0.9520 
                 0.0022 
               
               
                   
                 800 
                 80 
                 0.9531 
                 0.0015 
               
               
                   
                   
               
            
           
         
       
     
     In addition to Table 2,  FIG. 32  provides a graphical representation of the inverse proportion of the reflective and transmissive nature of the thin semi-reflective layer  443  based upon the thickness of the gold. Reflective and transmissive values used in the graph illustrated in  FIG. 32  are absolute values. 
       FIG. 33  is a top plan view of the transmissive type optical bio-disc  410  illustrated in  FIGS. 30 and 31  with the transparent cap portion  416  revealing fluidic channels  428 , inlet ports  422 , vent ports  424 , trigger marks  166 , and target zones  135  as situated within the disc. 
       FIG. 34  is an enlarged perspective view of optical bio-disc  410  according to the transmissive disc embodiment of the present invention. Disc  410  is illustrated with a portion of the various layers thereof cut away to illustrate a partial sectional view of each principle, layer, substrate, coating, or membrane.  FIG. 34  illustrates a transmissive disc format with the clear cap portion  416 , the thin semi-reflective layer  443  on the substrate  420 , and trigger marks  166 . Trigger marks  166  include opaque material placed on the top portion of the cap. Alternatively, trigger marks  166  may be formed by clear, non-reflective windows etched on the thin reflective layer  443  of the disc, or any mark that absorbs or does not reflect the signal coming from the trigger detector  160  ( FIG. 12 ).  FIG. 34  also shows, the target zones  135  formed by marking the designated area in the indicated shape or alternatively in any desired shape. Markings to indicate target zones  135  may be made on the thin semi-reflective layer  443 , on substrate  420 , or on the bottom portion of the substrate  420  (under the disc). Alternatively, target zones  135  may be formed by a masking technique that includes masking the entire thin semi-reflective layer  443  except the target zones  135 . In this embodiment, target zones  135  may be created by silk screening ink onto the thin semi-reflective layer  443 . An active layer  444  is applied over the thin semi-reflective layer  443 . In one preferred embodiment, active layer  444  is a thick layer of 2% polystyrene. Alternatively, polycarbonate, gold, activated glass, modified glass, or modified polystyrene such as polystyrene-co-maleic anhydride, may be used. In addition hydrogels can be used. As illustrated in this embodiment, adhesive or channel layer  418  is applied over active layer  444 . The exposed section of the adhesive layer  418  illustrates the cut out or stamped U-shaped form that creates fluidic circuits  428 . The final principle structural layer in this transmissive embodiment of the present bio-disc  410  is the clear, non-reflective cap portion  416  that includes inlet ports  422  and vent ports  424 . 
     Referring back to  FIG. 12 , in the case of the reflective bio-disc illustrated in  FIG. 29 , the return beam  139  is reflected from the reflective surface  446  (see  FIG. 35 ) of cap portion  416  of the optical bio-disc  410 . In this reflective embodiment of the present optical bio-disc  410 , the return beam  139  is detected and analyzed, for the presence of signal elements or agents, by a bottom detector  18  such as that illustrated in  FIG. 1 . This reflected return beam either alternately or simultaneously carries both operational information and information characteristic of the bio-bit, signal element, or investigational feature. In the transmissive bio-disc format, on the other hand, the transmitted beam  162  is detected, by a top detector  160 , and is also analyzed for the presence of signal agents. In the transmissive embodiment, a photo detector may be used as top detector  160 . The hardware triggering mechanism may be used in both reflective bio-discs ( FIG. 29 ) and transmissive bio-discs ( FIG. 34 ). 
       FIG. 35  is a partial cross sectional view of the reflective disc embodiment of optical bio-disc  410  according to the present invention.  FIG. 35  illustrates substrate  420  and reflective layer  442 . As indicated above, reflective layer  442  may be made from a material such as aluminum, gold or other suitable reflective material. In this embodiment, the top surface of substrate  420  is smooth.  FIG. 35  also shows active layer  444  applied over reflective layer  442 . Target zone  135  is formed by removing an area or portion of reflective layer  442  at a desired location or, alternatively, by masking the desired area prior to applying reflective layer  442 . As further illustrated in  FIG. 35 , adhesive layer  418  is applied over active layer  444 .  FIG. 35  also shows cap portion  416  and reflective surface  446  associated therewith. Thus when cap portion  416  is applied to adhesive layer  418 , which includes the desired cut-out shapes, flow channels  430  are thereby formed. Incident beam  137  is initially directed toward substrate  420  from below disc  410 , and then focused at a point proximate to reflective layer  442 . Since this focusing takes place in target zone  135  where a portion of reflective layer  442  is absent, incident beam  137  continues along a path through active layer  444  and into flow channel  430 . Incident beam  137  then continues upwardly traversing through flow channel  430  to eventually fall incident onto reflective surface  446 . At this point, incident beam  137  is returned or reflected back along the incident path and thereby forms the return beam  139 . 
       FIG. 36  is a partial cross sectional view of the transmissive embodiment of bio-disc  410  according to the present invention.  FIG. 36  illustrates a transmissive disc format with clear cap portion  416  and thin semi-reflective layer  443  on substrate  420 .  FIG. 36  also shows active layer  444  applied over thin semi-reflective layer  443 . In a preferred embodiment, the transmissive disc has thin semi-reflective layer  443  made from a metal such as aluminum or gold approximately 100–300 Angstroms thick and does not exceed 400 Angstroms. This thin semi-reflective layer  443  allows a portion of incident or interrogation beam  137 , from light source  19  ( FIG. 1 ), to penetrate and pass upwardly through the disc to be detected by top detector  160  ( FIG. 12 ), while some of the light is reflected back along the same path as the incident beam but in the opposite direction. In this arrangement, the return or reflected beam  139  is reflected from semi-reflective layer  443 . Thus in this manner, return beam  139  does not enter into flow channel  430 . The reflected light or return beam  139  may be used for tracking incident beam  137  on pre-recorded information tracks formed in or on the semi-reflective layer  443  as described in more detail in conjunction with  FIGS. 37 and 38 . In the disc embodiment illustrated in  FIG. 36 , a defined target zone  135  may or may not be present. Target zone  135  may be created by direct markings made on thin semi-reflective layer  443 , or on substrate  420 . These markings may be created using silk screening or any equivalent method. In the alternative embodiment where no physical indicia are employed to define a target zone, flow channel  430  is utilized as a confined target area in which inspection of an investigational feature is conducted. 
       FIG. 37  is a cross sectional view taken perpendicular to the tracks of the reflective disc embodiment of bio-disc  410  according to the present invention. This view is also taken longitudinally along a radius of a flow channel  430  of the disc. FIG.  37  includes substrate  420  and reflective layer  442 . In this embodiment, substrate  420  includes a series of grooves  118 , as best illustrated in  FIG. 3 . Grooves  118  are in the form of a spiral extending from near the center of the disc toward the outer edge. Grooves  118  are implemented so that interrogation beam  137  may track along the spiral grooves  118  on the disc. A raised or elevated portion  110  ( FIG. 3 ) separates adjacent grooves  170  in the spiral. The reflective layer  442  applied over grooves  118  in this embodiment is, as illustrated, conformal in nature.  FIG. 37  also shows active layer  444  applied over reflective layer  442 . Target zone  135  is formed by removing an area or portion of reflective layer  442  at a desired location or, alternatively, by masking the desired area prior to applying reflective layer  442 . As further illustrated in  FIG. 37 , adhesive layer  418  is applied over active layer  444 .  FIG. 37  also shows cap portion  416  and the reflective surface  446  associated therewith. Thus, when cap portion  416  is applied to adhesive layer  418 , which includes the desired cut-out shapes, flow channel  430  is thereby formed. 
       FIG. 38  is a cross sectional view taken perpendicular to the tracks of the transmissive disc embodiment of bio-disc  410  according to the present invention. This view is also taken longitudinally along a radius of a flow channel  430  of the disc.  FIG. 38  illustrates the substrate  420  and the thin semi-reflective layer  443 . Thin semi-reflective layer  443  allows a portion of the incident or interrogation beam  137 , from light source  19  ( FIGS. 1 and 12 ), to penetrate and pass through the disc to be detected by top detector  160 , while some of the light is reflected back in the form of return beam  139 . The thickness of thin semi-reflective layer  443  is determined by the minimum amount of reflected light required by the disc reader to maintain its tracking ability. In this embodiment, substrate  420 , like that discussed in  FIG. 37 , includes the series of grooves  118 . Grooves  118  in this embodiment are also preferably in the form of a spiral extending from near the center of the disc toward the outer edge. Grooves  118  are implemented so that interrogation beam  137  may track along the spiral.  FIG. 38  also shows active layer  444  applied over thin semi-reflective layer  443  with adhesive layer  418  applied overactive layer  444 .  FIG. 38  also shows cap portion  416  without a reflective surface  446 . Thus, when cap portion  416  is applied to adhesive layer  418 , which includes the desired cut-out shapes, flow channel  430  is thereby formed and a part of incident beam  137  is allowed to pass therethrough substantially unreflected. 
       FIG. 39  is a view similar to  FIG. 35  showing the entire thickness of the reflective disc and the initial refractive property thereof.  FIG. 40  is a view similar to  FIG. 36  showing the entire thickness of the transmissive disc and the initial refractive property thereof. Grooves  118  are not shown in  FIGS. 39 and 40  since the sections are cut along grooves  118 .  FIGS. 39 and 40  show narrow flow channel  430  situated perpendicular to the grooves  118  in these embodiments.  FIGS. 37 ,  38 ,  39 , and  40  show the entire thickness of the respective reflective and transmissive discs. In these figures, incident beam  137  is illustrated initially interacting with substrate  420  which has refractive properties that change the path of the incident beam as illustrated to provide focusing of beam  137  onto the reflective layer  442  or the thin semi-reflective layer  443 . 
     Optimizing the Optical Bio-Disc 
     A disc is optimized to provide a surface for detection of microscopic structures in an optical disc system. An optical disc is created for use in the optically corrected player previously discussed. The disc is manufactured as the “reverse image” or the forward image of a CD-Recordable disc, for example. Such optical discs and related manufacturing methods are further disclosed in commonly assigned U.S. patent application Ser. No. 10/005,313 entitled “Optical Discs for Measuring Analytes” filed Dec. 7, 2001, which is herein incorporated by reference. One such disc is the disc  130  illustrated in  FIG. 41  implemented as a “reverse wobble” disc. This embodiment of the disc  130 , includes the disc substrate  132  “reversed” as illustrated to form the cap or most distal layer. The disc further includes grooves  118  with bio-bits, signal elements, or investigation features  136  preferably situated therein. A non-integral cover  138  is then utilized as a proximal cap as shown relative to the incident beam  137 . 
     In the Compact Disc Recordable (CD-R) System, a laser is focused through a 1.2 mm polycarbonate (or similar refractive material) and is focused on a groove-like structure filled with dye materials that have absorption-effective properties. The disc manufactured for use in this detection system is manufactured as the “reverse image” of a CD-R disc. The reverse image allows the optical disc reader to interface with the first surface or air-interface of a continuous groove. The air-interface allows for a process that places microscopic structures on the surface that can be read. 
     The disc is manufactured using an electroforming or “Nickel Stamper” production method referred to as “Matrixing.” Once a nickel image has been created from the surface of an optical disc “Master,” it can be placed in an electroforming process (or similar process) and a reverse image can be created. The “Master” is often called the “Father” part. The “reverse image part” is often called the “Mother” part. In many CD manufacturing processes, the “Mother” part is used to produce another reverse image that is called the “Son” part. “Father” parts and “Son” parts have the same forward image. “Mother” parts have the reverse image. This process allows a master made from a normal CD-Recordable mastering process to be used for this application. It is technically feasible and possible to create “Father” parts with the correct forward image for this disc. The reverse image part is made of nickel and is utilized in an optical disc molding machine to create a plastic part representing the opposing image. 
     The reverse image part is more difficult to utilize in a CD manufacturing process because of its geometry. The edge of a forward image part is open and the edge of a reverse image part is closed. A mold must be designed for the CD molding process. This mold is provided with additional vents that allow the movement of polycarbonate or other remoldable refractive material to move properly across the surface of the nickel part. The venting design added to the mold will allow the desired optical discs to be created in a fashion similar to compact discs or CD-R discs. 
     The desired optical disc is designed with an optimized shape and form of the structure of a continuous groove that originates at the inner diameter and ends at the outer diameter of the disc. The groove depth is optimized to provide a very strong tracking magnitude (push-pull signal). The depth of the manufactured groove is very close to ⅛ of the wavelength λ of the laser light incident on the air interface of the optical disc. The depth of the manufactured groove can also be odd multiples of these values (e.g., ⅛λ, ⅜λ, ⅝λ, etc.). The width of the optical disc groove is optimized to facilitate placement or size detection of the structures that will be placed on the surface of the optical disc. Thus in one preferred embodiment, a ⅛ wave push-pull tracking derivation is employed. The slope of the groove structure is optimized to provide for an optimal focusing position in the groove and for an optimized tracking signal response. Optimization of the land areas within the continuous groove is performed to reduce signal cross-talk and to optimize structure detection. 
     The air-incident surface of the optical disc is manufactured to provide light contrast to the microscopic structures that will be placed on the surface of the disc. If the structures absorb light, a reflective material (such as gold) is placed on the air-incident surface. If the structures reflect light, a non-reflective material will be placed on the air-incident surface. The discs are manufactured to provide optimal mechanical performance in a CD recordable player. 
     The air-incident surface of the reverse image disc provides the required operational requirements of the optically corrected player discussed previously. The adjustment lens will allow the reverse image disc to perform similarly to a non-recorded CD-R disc. This test mode is available through the software interface of a consumer CD-R drive. The player can be placed in a test mode and will track the “wobbled” groove through the information area. The location of a component on the surface of the wobbled groove can be detected to 1/75 of a second by utilizing the consumer CD-R wobbled groove format. The locational information in the consumer CD-R format is contained in the mastered “wobble” signal and can be secured through the software interface to a consumer drive. Microscopic structures placed on the surface of the reverse image disc will not have an effect on the operational requirements of a wobble groove system until they reach a very high concentration (point of data gathering). In effect, the wobble groove allows for placement of microscopic structures on the surface of the optical disc without having an adverse effect on the operational requirements of the CD-R system. 
     The characteristics of the structures placed on the surface of the reverse image disc can now be detected by monitoring the quad sum signal of the CD-R objective assembly. The electrical response of these microscopic structures can also be detected in the electrical signal applied to the focusing servo, the tracking servo, and the power control monitoring system. The characteristics of the head movement in the radial and tangential plane parallel to the surface of the reverse image disc can be detected in the electrical signal applied to the tracking servo circuitry. The characteristics of the head movement in the vertical plane perpendicular to the surface of the reverse image disc can be detected on the electrical signal applied to the focusing servo circuitry. These signals can be cross-referenced to the information gathered by the quad sum signal and the power-monitoring signal. The information for each of these responses can be analyzed in a mathematical format to relate dimensional characteristics of the microscopic structure detected on the surface in the reverse image disc. An application of Differential Mathematics or Vector analysis can be applied to extract the characteristics of each microscopic structure. 
     Structures on the surface of the reverse image disc can be designed for maximum detection resolution by designing a placement and dimensional requirement to remain within the focal position of the laser spot. The microscopic structures should be designed for maximal optical contrast with the surface of the reverse image disc to provide for strong signal detection and low electrical CNR. Microscopic structures applied to the surface of the reverse image disc should be small enough to remain within the focusing plane of the laser spot. As the dimensional characteristics overcome the focal position, a smaller portion of the signal is detected in the quad sum detector, while a larger portion of the signal is detected in the other operational servos. 
     The disc may be designed with a specialty groove that would accommodate the dimensional aspects of the microscopic structures. The microscopic structures can be designed for placement inside the grooves of the reverse image disc. This would be used to further optimize the quantifiable detection characteristics of the system. The microscopic structures are created in a “spherical shape.” These spheres, when placed on the surface of the reverse image disc, generate a very characteristic electrical response in the servo and operational signals in the drive. The land areas of the disc (the areas between the grooves) are created with a smooth round surface, which will allow the spheres to fall into a holding position within the groove that is easily detected by the electrical signals. 
     The reporter spheres or bio-bits may be created with a diameter that is smaller than the width of the groove as discussed above. This allows the spheres to enter the groove and facilitates detection as represented in  FIG. 41 . The spheres can also be formed out of a compressible material and have a diameter that is slightly larger than the width of the groove. In one embodiment, an adaptable plate is used to compress the spheres and drive them into the groove. 
     Having described certain embodiments, it should become apparent that modifications could be made without departing from the scope of the claims as set out below. For example, the terms over and under are used for reference purposes and not absolute positioning. 
     Investigational Features 
     The structures, features, characteristics, and attributes that are investigated according to the present invention may include biological, chemical, or organic specimens, test samples, investigational objects such as parts of insects or organic material, and similar test objects or target samples. Such structures, features, and attributes may also, include specific chemical reactions and the products and/or by-products resulting therefrom such as, for example, any one of a variety of different colorimetric assays. In the case of an optical bio-disc, the material applied to the disc for investigation and analysis may include biological particulate suspensions and organic material such as blood, urine, saliva, amniotic fluid, skin cells, cerebrospinal fluid, serum, synovial fluid, semen, single-stranded and double-stranded DNA, pleural fluid, cells from selected body organs to tissue pericardial fluid, feces, peritoneal fluid, and calculi. In the case of some of these materials, a reporter may be employed for detection purposes. Reporters useful in the invention described herein include, but are not limited to, plastic micro-spheres or beads made of, for example, latex, polystyrene, or colloidal gold particles with coatings of bio-molecules that have an affinity for a given material such as a biotin molecule in a strand of DNA. Appropriate coatings include those made from streptavidin or neutravidin, for example. In this manner, objects too small to be detected by the read beam of the drive may still be detected by association with the reporter. 
     An optical disc playback device can be used to detect features and surface characteristics in the focusing plane of an optical disc. Microscopic structures, cells, reporters, or “bio-bits” are added to a focusing plane in the optical disc assembly so that they can be detected in the electrical signals that are generated when the laser light reflected or transmitted from the surface of the optical disc is collected by the objective assembly and/or a top detector. The microscopic structures and the optical disc platform are designed to promote accurate detection and to have a minimal effect on the operational requirements of the system. 
     Small biological and/or spherical structures are measured on the surface or within the focusing planes described as follows. These structures are physically larger than one-half the wavelength of the light used to detect them (the light incident on the structures). 
     When these microscopic structures or bio-bits exist on the surface of the optical disc focal plane, the structures will appear on the surface of the land areas. Signal elements, bio-bits, or investigational features may also exist on a plane that is not within the immediate field of focus but is very near. In this case, the structures are close enough to the field of focus to be detectable by the reflected laser light. Investigational features such as bio-bits can also exist on multiple planes that are separated from the laser that is fulfilling the operational requirements of characterization of the structures. The bio-bits and other reporters may also be inserted into the groove or pits and cause enough optical interference in the reflected signal to generate a confident detection signal. Bio-bits can also exist within areas that are logically zoned or organized by the manufacturing of the disc. These areas may be land-level or pit-level, and may be very large (e.g., DVD-RAM). 
     Detecting Investigational Features 
     Investigational features, such as reporters or blood cells, produce a signal level or density change relative to a signal produced by reading information encoded on the disc. Commonly assigned and co-pending U.S. patent application Ser. No. 09/421,870 entitled “Trackable Optical Discs with Concurrently Readable Nonoperational Features” filed Oct. 26, 1999, herein incorporated by reference, teaches that micron-sized investigational or “non-operational” structures may be disposed upon a surface of an optical disc in a number of ways. One suitable embodiment for accomplishing this is depicted in  FIG. 41  as discussed above. As shown in  FIG. 41 , light beam  137  is incident upon the disc assembly  130  from below. Disc  130  includes disc substrate  132  and reflective layer  134 , upon which investigational structures or features  136  are disposed. Wobble grooves  118 , impressed in substrate  132  and coated by reflective layer  134 , are indicated in  FIG. 41 . Also shown is the non-integral cover  138 . Investigational structures  136  may be detected, measured, and characterized by the optical disc reader according to the present invention. The operational structures of the disc, including tracking features, may be detected concurrently (or non-concurrently) with, and readily discriminated from, investigational structures using a single optical pickup. 
     With reference next to  FIG. 42 , a view similar to  FIG. 5  discussed above, there is shown three light spots that are produced by a typical three-beam optical design incident on an optical disc assembly having pits  60 . Laser beam spots  62 ,  64 , and  66  are illustrated as dashed lines on the surface of the optical disc. These beams can be focused on the same surface of the disc as pits  60 , or on any other outer surface or inner surface of the disc. These beams can also be focused on different layers of the disc, a “layer” referring to any portion of the disc that has a finite thickness such as in the multi-layer discs disclosed in U.S. patent application Ser. No. 10/006,620 referenced above. 
     In a three-beam optical disc system, detectors A, B, C, and D, as shown in  FIG. 4 , are configured to detect light reflected from beam spot  62 , as shown in  FIG. 42 . Also, detectors E and F are independently configured to detect the reflected light from beam spots  64  and  66 , respectively. As mentioned above, this configuration has been implemented such that focus and synchronization information are provided by light reflected at beam spot  62  and the tracking information is provided by light reflected at beam spots  64  and  66 . 
       FIG. 43  shows an investigational feature  68  disposed on a surface of an exemplary optical disc assembly. In this arrangement, beam spot  62  can be used to detect operational structures (e.g., pits) for tracking, focus, and synchronization and beam spot  66  can be used simultaneously to detect one or more investigational features  68 . Alternatively, beam spot  64  may be used to detect investigational feature  68 , depending on the size and location of investigational feature  68 . 
     Also, if investigational feature  68  is sufficiently large, beam spots  64  and  66  can be used in combination (though not necessarily simultaneously) for detecting investigational feature  68 . It will be appreciated that a combination of patterns from each of the beam spots can be used to detect the size and position of investigational feature  68 . Also, patterns from detectors A, B, C, and D can be combined with patterns from one or both of detectors E and F to determine the size and position of the investigational features. Thus, a single objective assembly can detect different optical paths of operational structures and investigational features. It will be appreciated that the invention disclosed herein relates to the detection of operational and investigational features and is not limited to an optical disc assembly having a pits and lands format. Rather, the invention can be used with any other format such as those discussed above. 
       FIG. 44  is a graph illustrating a representative relative displacement of the data signal (or density) when the read beam of the drive encounters such an investigational feature on or in the disc. The data signal may be the HF signal, the tacking error signal, the focus error signal, or one or more of a variety of other different signals such as those identified above. 
     In  FIGS. 45 and 46 , a change in an “operational” feature such as a groove, pit or land, produces a change in signal level, signal jitter, or error rate. In  FIG. 45 , a section view of a pit, the pit produces a change in signals A and B from the detector of the disc reader, and, when added, an unusual fluctuation is produced. In  FIG. 46 , a plan view of a pit, a lateral displacement produces a net displacement in the tracking error signal (TE signal). 
     An increase or decrease in reflectivity is produced when the incident beam interacts with the disc. This change in reflectivity can be monitored by a corresponding change in the Automatic Gain Control (“AGC”) setting, which is output at the drive port. Thus, in accordance with the present invention, when the read or “interrogation” beam of the drive encounters an investigational feature, a change in return light is monitored. 
     The structure of an optical disc can be anything from a surface with pits and lands, a surface with a continuous wobbled groove, a surface containing a phase contrast hologram, a surface with a combination of pits/grooves or a surface with nothing on it. As discussed previously, reporters, bio-bits, or cellular structures can be measured in many different focusing planes. Bio-bits can also be detected and characterized by multiple lasers, multiple objective assemblies, and multiple laser wavelengths. 
     Reporters, bio-bits, and cellular structures could be located on the primary surface of a holographic disc. Further details relating to this use of holograms is disclosed in U.S. patent application Ser. No. 10/005,313. The information gathered from the hologram is used for operational characteristics. Bio-bits can be put as close to or as far away from the operational plane as needed. The refractive layer (polycarbonate, polymethyl acrylic or glass) can be adjusted to optimize the desired optical properties of the detection laser. 
     Alternatively, investigational features may include a chemical reaction, taking place in a flow channel, such as flow channel  430  shown in  FIG. 27 , formed on or in the disc as illustrated in  FIG. 47 . In this embodiment, the reflectivity, operational features, or interference patterns on an optical disc are affected by a chemical deposition or reaction. The disc is manufactured with a very low error rate or a known error rate that acts as a data “mask.” The data pattern on the disc is designed to produce a logical or physical enhancement to the errors produced by investigational features or groupings of a specific size range. 
     For example, the interleaving distance can be adjusted in the mastering logic to enhance the burst error response to a specific feature, size, or density distribution. A data pattern is written on the disc to produce as a response to specific feature sizes or density distribution. These may include, but are not limited to, the following: 
     1. a non-pause; 
     2. a sound signal (response to digital silence encoding); 
     3. a specific error correction pattern or distribution (e.g., E11, E21, E31, burst, E12, E22, E32, E42); 
     4. an uncorrectable error; 
     5. an ECC/EDC count; 
     6. an inner or outer parity error; 
     7. a CRC error in the wobble signal decoder; 
     8. a sector error (75/sec); or 
     9. a block error (7350/sec). 
     In an exemplary embodiment, a fluidic channel is placed within a disc. The disc can have up to 99 tracks with grooves, pits, or a combination of operational features for CD, CD-R, DVD, DVD-RAM, DVD-R, DVD-RW. A specific chemical reaction or deposition of “non-ops” (spheres, metallics, etc.) will enhance or remove material from the metallic reflective layer or the operational or focal plane. Spots or zones are placed on the disc in different bands or tracks. Logic in each band determines the position of the objective assembly. Logic can also determine the “software servo response.” Starting with low-density distribution or effect, spots are placed in increasing density and increasing radius positions in each bank or track. On a DVD-RAM disc or similar, the spots are placed within the Zones (Zoned CLF system). The reaction will produce physical changes in the “ops features,” inducing errors or error sites on the disc at each location. The digital, analog, optical, mechanical, and logical responses may be evaluated to characterize the effect. 
     In this embodiment, each site has increasing error rates and an attempt is made to correlate to the error distributions: E11, E21, E31, Burst, E12, E22, E32, E42, Uncorrectable, Unrecoverable, ECC/EDC, or BLER. In a preferred embodiment, the process is started with low-density distributions and moved to higher distributions until a correlation is discovered between the analyte concentration and the error distribution. The disc is advantageously mastered to enhance the correlation. For example, interleaving is modified or changed to enhance the Burst and C2 response. 
     Reaction with the surface, operational plane, or focal plane of the disc creates and increases or decreases analog signal level or density. The reaction will produce a change in reflectivity or signal density, either a reduction or increase in reflective layer, or a change in shape and/or size of phase/interference features (pits or lands). 
     As a general proposition, the reflectivity of a metal layer is a function of the thickness of the layer up to a certain threshold thickness as discussed above in connection with  FIG. 32 . For a variety of different metals such as nickel, aluminum, silver, or gold, as represented in  FIG. 48 , reflectivity is unchanging and remains essentially constant at between about 80% and nearly 100% for a metal thickness equal to or greater than a threshold thickness. This reflectivity also depends on metal purity and surface conditions. As a general matter relating to certain specific aspects of the present invention, a metal film thickness and surface condition can be altered when a metal film such as reflective layer  443  (as best illustrated in  FIG. 34 ) reacts with a fluid contained in flow channels of the disc. 
     In  FIG. 49 , the chemical reaction occurring in the flow channel  430  of the disc illustrated in  FIG. 47  causes fluctuations in signals being monitored, for example, the HF or TE signal. When the interrogation beam  137  of a disc drive traverses across a chemical reaction occurring in or on the disc, the envelope of the signal fluctuations increases or decreases with reaction time. 
     According to another aspect of the present invention, pits, marks, or grooves on a disc can be made of a chemically interactive material. The level of degradation in the material can determine some assay characteristics by providing a change in signal response. Chemistry or assay material can react with the reflective layer and reduce or enhance light transmitted, reflected, refracted, or absorbed according to the change in reflectivity of the reflective or metal layer  443  shown in  FIG. 47 . For example, operational structures may be made of a nitrated cellulose material. Chemical interactions may change the shape and/or thickness of operational structures, and thus, reduce signal response. Also the pH of the solution may cause a deposition of metal on the surface of a zone in the disc and produce an increase in localized reflectivity. In another implementation, localized reactions may cause the removal of metallic material from the reflective surface. The removal of the material will cause a point of contrast in the signal. The response may be an analog signal characterization or an error rate distribution. Additionally, zones may be designed into the disc for differing concentrations and reactions. In these embodiments, the material is designed in such a way as to degrade at a specific concentration or reaction level. 
       FIG. 50  generally represents these aspects of the present invention. The disc in  FIG. 50  includes zones A, B, and C that are formed, for example, on a DVD-RAM disc with Zoned Constant Linear Velocity, (ZCLV). Zone C included a reaction according to this aspect of the present invention where the reflective layer was removed, while in zones A and B no such metal-removing reaction occurred. The resulting signal traces of, for example, the HF or TE signals are also shown. The signal traces reveal that traces across the zones with the reflective material intact generated a detectable signal, while the scan across the zone without reflective material did not. 
     With reference now to  FIG. 51 , there is shown a cross-sectional side view of an optical bio-disc  200  that includes bead reporters  210  as utilized in conjunction with the present invention. Bio-disc  200  includes substrate  202 , metal film layer  204 , an adhesive or channel layer  206 , and cover disc  208 . Substrate  202  includes pits or groves or other means on which information may be encoded in known ways. Substrate  202  is generally covered with metal film layer  204  in areas over which information is encoded. However, bio-disc  200  differs from known information discs (e.g., music, DVD, etc.) in that the bio-disc includes an investigational structure (in this case bead reporters) over a part of the disc. Chemical layer  214  (e.g., antibodies) is deposited in a desired target area of the disc. Each bead reporter  210  also has a surface coated with a similar or identical chemical layer  212 . The bead reporters  210  are small plastic spheres (or other material spheres) that are coated with a chemical agent to interact with biological chemicals in a solution. 
     As a specific example of one aspect of the present invention,  FIG. 52A  presents a graphical representation of two 6.8 μm blue beads positioned relative to several tracks (labeled A through H) of an optical bio-disc according to this invention. These beads were located on and adhered to a disc similar to the disc shown in  FIG. 51 . Scan traces A through H are depicted, several of which pass over the bead reporters. 
       FIG. 52B  is a series of signature traces including distinctive signal perturbations derived from the bead reporters of  FIG. 52A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 52B  reveals that a scan over two 6.8 μm reporter beads results in distinct perturbations of the HF signal that can be detected. 
     As another particular example,  FIG. 53A  presents a graphical representation of two 6.42 μm red beads positioned relative to the tracks of an optical bio-disc according to the present invention. These beads were located on a disc similar to the disc shown in  FIG. 51 . 
       FIG. 53B  is a series of signature traces derived from the beads of  FIG. 53A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to an ADC  150  and is processed by PC  158  and imaged by display  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 53B  reveals that a scan over two 6.42 μm reporter beads results in distinct perturbations of the HF signal that can be detected. 
     As yet another example according to the present invention,  FIG. 54A  presents a graphical representation of two 6.33 μm polystyrene beads positioned relative to the tracks of an optical bio-disc according to the present invention. These beads were located on a disc similar to the disc shown in  FIG. 51 . 
       FIG. 54B  is a series of signature traces and related signal perturbations derived from the beads of  FIG. 54A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  (see  FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to an ADC  150  and is processed by PC  158  and imaged by monitor  146  (see  FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 54B  reveals that a scan over two 6.33 μm polystyrene reporter beads results in distinct perturbations of the HF signal that can be detected. 
     As yet still another example of certain aspects of the present invention,  FIG. 55A  presents a graphical representation of a 5.5 μm glass reporter bead positioned relative to the tracks of an optical bio-disc according to this invention. This bead was located on a disc similar to the disc shown in  FIG. 51 . 
       FIG. 55B  is a series of signature traces derived from the bead illustrated in  FIG. 55A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 55B  reveals that a scan over a 5.5 μm glass reporter bead results in a perturbation of the HF signal that can be detected. 
     Another example of this invention is presented in  FIG. 56A  which shows a graphical representation of a 4.5 μm magnetic bead positioned relative to the tracks of an optical bio-disc according to the present invention. This bead was located on a disc similar to the disc shown in  FIG. 51 . 
       FIG. 56B  is a series of signature traces derived from the bead illustrated in  FIG. 56A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 56B  reveals that a scan over a 4.5 μm magnetic reporter bead results in a perturbation of the HF signal that can be detected. 
       FIG. 57A  is a graphical representation of two actual 4.0 μm blue beads positioned relative to the tracks of an optical bio-disc according to another example of certain aspects of the present invention. These beads were located on a disc similar to the disc shown in  FIG. 51 . 
       FIG. 57B  is a series of signature traces and related signal perturbations derived from the beads of  FIG. 57A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 57B  reveals that a scan over two 4.0 μm reporter beads results in a perturbation of the HF signal that can be detected. 
     As yet a further example hereof,  FIG. 58A  shows a graphical representation of a 2.986 μm polystyrene bead positioned relative to the tracks of an optical bio-disc according to the present invention. This bead was located on a disc similar to the disc shown in  FIG. 51 . 
       FIG. 58B  is a series of signature traces derived from the bead illustrated in  FIG. 58A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 58B  reveals that a scan over a 2.986 μm polystyrene reporter bead results in a perturbation of the HF signal that can be detected. 
     An yet still as a further example of this invention,  FIG. 59A  presents a graphical representation of two 2.9 μm white beads positioned relative to the tracks of an optical bio-disc according to the present invention. These beads were located on a disc similar to the disc shown in  FIG. 51 . 
       FIG. 59B  is a series of signature traces derived from the beads of  FIG. 59A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 59B  reveals that a scan over two 2.9 μm reporter beads results in distinct signal perturbations of the HF signal that can be detected. 
       FIG. 60A  is a graphical representation of four 2.8 μm magnetic beads positioned relative to the tracks of an optical bio-disc according to another specific example of certain aspects of this invention. These beads were located on a disc similar to the disc shown in  FIG. 51 . 
       FIG. 60B  is a series of signature traces derived from the beads of  FIG. 60A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 60B  reveals that a scan over four 2.8 μm magnetic reporter beads results in distinct perturbations of the HF signal that can be detected. 
     As another example,  FIG. 61A  presents a graphical representation of a mixture of beads including 2.8 μm magnetic beads, 4.0 and 6.8 μm blue polystyrene beads, and different sized silica beads positioned relative to the tracks of an optical bio-disc according to the present invention. These beads were located on a disc similar to the disc shown in  FIG. 51 . 
       FIG. 61B  is a series of signature traces and related signal perturbations derived from the beads of  FIG. 61A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 61B  reveals that a scan over the mixture of reporter beads results in distinct perturbations of the HF signal that can be detected. 
       FIG. 62A  is a graphical representation of two 2.9 μm white fluorescent polystyrene beads positioned relative to the tracks of an optical bio-disc according to the present invention. These beads were located on a disc similar to the disc shown in  FIG. 51  and in this example a DC coupled signal is utilized rather than the AC coupled signal discussed in connection with the example traces illustrated in  FIGS. 52B through 61B . 
       FIG. 62B  is a series of signature traces derived from the beads of  FIG. 62A  utilizing a DC coupled and buffered HF signal from the optical drive according to the present invention. The HF-DC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24A ) then directed to output connector J 5  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 62B  reveals that a scan over two 2.9 μm white fluorescent polystyrene beads results in distinct perturbations of the HF-DC signal that can be detected. 
       FIG. 63A  is a graphical representation of two 2.9 μm white fluorescent polystyrene beads, as illustrated in  FIG. 62A , positioned relative to the tracks of an optical bio-disc according to the present invention. These beads were located on a disc similar to the disc shown in  FIG. 51 . In this example, a DC coupled and buffered “A” signal is employed to obtain the desired signal traces as discussed in further detail immediately below. 
       FIG. 63B  is a series of signature traces derived from the beads of  FIG. 63A  utilizing the DC coupled and buffered “A” signal from the optical drive according to the present invention. The HF-A coupled signal ( FIG. 22 ) from optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIGS. 24B and 24C ) then directed to output connector J 7  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  (see  FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 63B  reveals that a scan over two 2.9 μm white fluorescent polystyrene beads results in distinct perturbations of the HF-A signal that can be detected. 
       FIGS. 64A and 64B  are the same cross-sectional side view of optical bio-disc  200  ( FIG. 51 ) showing the biochemical interaction between the bio-disc and the reporter beads in greater detail. 
       FIG. 64A  shows greater detail of chemical layer  214  disposed over metal film over metal film layer  204 . Chemical layer  212  is also shown coated over reporter beads  210 . In  FIG. 64B , the beads are mixed with the biological solution containing investigational feature  216 , and injected into or otherwise applied to bio-disc  200  between substrate  202  and cover  208 . Both the chemical layer  212  on the surface of the bead reporters  210  and chemical layer  214  attract and adhere to investigational feature  216 . In this way, if the chemical under investigation (i.e., investigational feature) is present in the biological solution, the chemical under investigation becomes a bonding agent to bond the bead reporters  210  to substrate  202 . When bio-disc  200  is spun up, it acts like a centrifuge. Bead reporters that are not bonded will be forced to an outer periphery of the disc, and bonded bead reporters will remain uniformly distributed over the area of the disc coated with chemical layer  204 . It then remains only to decide whether the bead reporters have been swept to an outer periphery of the disc. Examples of such bead-based assay discs and methods of use are described in commonly assigned U.S. Provisional Applications: No. 60/257,705, titled “Surface Assembly for Immobilizing DNA Capture Probes and Bead-Based Assay Including Optical Bio-Discs and Methods Relating Thereto,” filed Dec. 22, 2000; No. 60/292,110, titled “Surface Assembly for Immobilizing DNA Capture Probes using Pellets as Reporters in Genetic Assays Including Optical Bio-Discs and Methods Relating Thereto,” filed May 18, 2001; and No. 60/302,757, titled “Clinical Diagnostic Optical Bio-Disc and Related Methods for Selection and Detection of Lymphocytes Including Helper-Inducer/Suppressor-Cytotoxic Cells,” filed Jul. 3, 2001. By the above examples, the inventors have illustrated that discernable signals of investigational features may be readily detected using reporter beads as described herein. 
       FIG. 65  is a cross-sectional side view of an optical bio-disc  190  including a proximally positioned red blood cell  199  as the investigational feature interrogated by the read beam  191  of the optical disc drive assembly according to the present invention. 
     Bio-disc  190  includes substrate  192 , metal film layer  194 , adhesive or channel layer  196 , and cover disc  198 . Substrate  192  includes pits, groves, or other means on which information may be encoded in ways known in the art. Substrate  192  is generally covered with metal film layer  194  in areas over which information is encoded. However, bio-disc  190  differs from known information discs (e.g., music, DVD, etc.) in that the bio-disc includes an investigational structure (in this case, a blood cell  199 ) over a part of the disc. Metal film layer  194  is removed from areas to be used for investigational structures. Capture agent  195  (e.g., antibodies) is deposited in the area of the removed metal film layer. Blood cell  199  may include a biological chemical under investigation (e.g., a chemical unique for blood type A or type B) that has an affinity for capture agent  195 . In this way, if the chemical under investigation is present in the biological specimen, the chemical under investigation becomes a binding agent to bind blood cell  199  to substrate  192 . When bio-disc  190  is spun in an optical disc drive, the resulting centrifugal force sends blood cells that are not bound to an outer periphery of the disc, while bound blood cells remain distributed over the area of the disc coated with capture agent  195 . The bound cells are then detected and quantified using an optical disc reader. Further details relating to this type of on-disc blood typing assays are disclosed in commonly assigned, co-pending U.S. patent application Ser. No. 09/988,850 entitled “Methods and Apparatus for Blood Typing with Optical Bio-Discs” filed Nov. 19, 2001, which is herein incorporated by reference. 
     As an example of detection of a cell reporter according to certain aspects of the present invention,  FIG. 66A  presents a graphical representation of proximally positioned red blood cell  199 , approximately 6.0 μm in diameter, positioned relative to the tracks of the optical bio-disc  190  illustrated in  FIG. 65 . 
       FIG. 66B  is a series of signature traces derived from the red blood cell of  FIG. 66A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 66B  reveals that a scan over a proximally positioned red blood cell results in a perturbation of the HF-AC coupled signal that can be detected. 
       FIG. 67A  is a graphical representation of a proximally positioned red blood cell approximately 6.0 μm in diameter positioned relative to the tracks of an optical bio-disc according to the present invention. For this example, the red blood cell illustrated in  FIG. 67A  was located on the type of the disc shown in  FIG. 65 . 
       FIG. 67B  is a series of signature traces derived from the red blood cell of  FIG. 67A  utilizing a DC coupled and buffered HF signal from the optical drive according to the present invention. The HF-DC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24A ) then directed to output connector J 5  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 67B  reveals that a scan over a proximally positioned red blood cell results in a perturbation of the HF-DC signal that can be detected. 
       FIG. 68  is a cross-sectional side view of an optical bio-disc  190  similar to the disc shown in  FIG. 65 , including a distally positioned red blood cell  199  as the investigational feature interrogated by read beam  191  of the optical disc drive assembly according to the present invention. 
     Bio-disc  190  includes substrate  192 , metal film layer  194 , adhesive or channel layer  196 , and cover disc  198 . Substrate  192  generally includes pits or groves or other means on which information may be encoded in known ways except over areas in which investigational structures are to be located. Substrate  192  is generally covered with metal film layer  194  in areas over which information is encoded but not in areas in which investigational structures are to be located. Bio-disc  190  differs from known information discs (e.g., music, DVD, etc.) in that the bio-disc includes an investigational structure (in this case, a blood cell  199 ) over a part of the disc. Metal film layer  194  is removed from areas to be used for investigational structures. Capture agent  195  (e.g., antibodies) is deposited in the area on cover disc  198  opposite the removed metal film layer. Blood cell  199  may include a biological chemical under investigation (e.g., a chemical unique for blood type A or type B) that is attracted to and adheres to capture agent  195 . In this way, if the chemical under investigation is present in the biological specimen, the chemical under investigation becomes a binding agent to bind blood cell  199  to disc cover  198 . When bio-disc  190  is spun in an optical disc drive, the resulting centrifugal force sends unbound blood cells to an outer periphery of the disc, while bound blood cells remain distributed over the area of the disc coated with capture agent  195 . The bound cells can be detected and quantified using an optical disc reader as further described in U.S. patent application Ser. No. 09/988,850 referenced above. 
       FIG. 69A  is a graphical representation of two distally positioned red blood cells approximately 6.0 μm in diameter positioned relative to the tracks of an optical bio-disc according to this example of these aspects of the present invention. The red blood cells illustrated in  FIG. 69A  were located on the type of the disc shown in  FIG. 68 . 
       FIG. 69B  is a series of signature traces derived from the red blood cells of  FIG. 69A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to connector output J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 69B  reveals that a scan over two distally positioned red blood cells results in distinct perturbations of the HF-AC coupled signal that can be detected. 
       FIG. 70A  is a graphical representation of the two distally positioned red blood cells illustrated in  FIG. 69A . The red blood cells illustrated in  FIG. 70A  were located on the type of the disc shown in  FIG. 68 . 
     As yet a further example of certain aspects of this invention,  FIG. 70B  presents a series of signature traces derived from the red blood cells of  FIG. 70A  utilizing a DC coupled and buffered HF signal from the optical drive according to the present invention. The HF-DC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24A ) then directed to output connector J 5  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 70B  reveals that a scan over two distally positioned red blood cell results in distinct perturbations of the HF-DC signal that can be detected. 
       FIG. 71  is a top perspective view of an optical inspection disc  220  with the top cap removed to illustrate a gnat&#39;s wing  222  positioned in an inspection channel  224  according to the present invention. Optical inspection disc  220  illustrated in  FIG. 71  also includes a trigger mark  166 . Trigger mark  166  provides the same function as the trigger mark  166  discussed in detail in conjunction with  FIGS. 12 and 13 . 
       FIG. 71A  is an enlarged top view of the indicated portion of  FIG. 71  showing in greater detail gnat&#39;s wing  222 , inspection channel  224 , and information storage tracks  226  of the optical inspection disc  220  according to this embodiment of the present invention.  FIG. 71A  also shows a focused spot  227  of the incident beam directed toward the gnats wing  222 . 
       FIG. 72  is a cross-sectional side view taken perpendicular to a radius of optical inspection disc  220  of  FIG. 71  including gnat&#39;s wing  222  as the investigational feature located within inspection channel  224 . Gnat&#39;s wing  222  is interrogated according to the present invention by read beam  225  of an optical disc drive assembly. 
       FIG. 73A  is a graphical representation of a lateral section of the gnat&#39;s wing  222  of  FIG. 71  as positioned in inspection channel  224  relative to tracks  226  of optical inspection disc  220  according to the present invention. 
       FIG. 73B  is a single signature trace derived from the section of the gnat&#39;s wing of  FIG. 73A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 73B  reveals that a scan over an investigational feature such as gnat&#39;s wing  222  results in a perturbation of the HF signal that can be detected. 
       FIG. 74A  is a similar graphical representation of a lateral section of gnat&#39;s wing  222  of  FIG. 71  as positioned in inspection channel  224  relative to tracks  226  of optical inspection disc  220  according to the present invention. 
       FIG. 74B  is a series of four consecutive signature traces derived from the section of the gnat&#39;s wing of  FIG. 74A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  (see  FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 74B  reveals that consecutive traces, scanned over an investigational feature such as gnat&#39;s wing  222 , result in distinct perturbations of the HF signal that can be detected. 
       FIG. 75A  is a similar graphical representation of a lateral section of gnat&#39;s wing  222  of  FIG. 71  as positioned in inspection channel  224  relative to tracks  226  of optical inspection disc  220  according to the present invention. 
       FIG. 75B  is a series of consecutive signature traces at moderate density derived from the section of the gnat&#39;s wing of  FIG. 75A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 75B  reveals that consecutive traces at moderate density, scanned over an investigational feature such as gnat&#39;s wing  222 , result in distinct perturbations of the HF-AC signal that can be detected. 
       FIG. 76A  is a similar graphical representation of a lateral section of gnat&#39;s wing  222  of  FIG. 71  as positioned in inspection channel  224  relative to tracks  226  of optical inspection disc  220  according to the present invention. 
       FIG. 76B  is a series of consecutive signature traces at higher density derived from the section of the gnat&#39;s wing of  FIG. 76A  utilizing an AC coupled and buffered HF signal from the optical drive according to the present invention. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signal is sent to ADC  150  and is processed by PC  158  and imaged by monitor  146  (see  FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIG. 76B  reveals that consecutive traces at higher density, scanned over an investigational feature such as gnat&#39;s wing  222 , result in distinct perturbations of the HF signal that can be detected and imaged. 
       FIGS. 77A ,  77 B, and  77 C are pictorial representations of the gnat&#39;s wing of  FIG. 71  as rendered by imaging methods according to the present invention respectively utilizing either an AC coupled and buffered HF signal, a DC coupled and buffered “A” signal, or a DC coupled and buffered HF signal from an optical drive assembly. The HF-AC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24B ) then directed to output connector J 3  of output section  157  ( FIG. 22 ). 
     The HF-A coupled signal ( FIG. 21 ) from optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIGS. 24B and 24C ) then directed to output connector J 7  of output section  157  ( FIG. 22 ). 
     The HF-DC coupled signal from HF Matrix Amp  18 A ( FIG. 21 ) of optical head assembly  174  ( FIG. 19 ) is directed to buffer amplifier card  152  ( FIGS. 22 and 23 ). The signal is amplified and conditioned ( FIG. 24A ) then directed to output connector J 5  of output section  157  ( FIG. 22 ). From buffer amplifier card  152 , the signals are sent to ADC  150  and are processed by PC  158  and imaged by monitor  146  ( FIGS. 9A and 12 ). As described above, modified PC  142  may substitute one or more of the processing devices described herein.  FIGS. 77A ,  77 B, and  77 C reveal that scans utilizing different signals produced by the optical head assembly of the disc drive render pictorial representations of the investigational feature that are detectable. 
       FIG. 78  is a graphical representation illustrating the relationship between  FIGS. 78A and 78B . 
       FIGS. 78A and 78B  are electrical schematics of a second embodiment of the amplifier stages that may be implemented according to the present invention in the buffer cards shown in  FIGS. 22 and 23 . 
       FIG. 78A  is a partial electrical schematic of the buffer amplifier. The analog HF-A signal from the optical head assembly  174  ( FIG. 19 ) is taken from pins  19  and  14  of connector  155  ( FIGS. 22 and 23 ). The input signal travels across an input load resistor and a voltage, stabilization capacitor to equalize background noise between the positive and negative leads. The positive signal is then fed into an op amp, which is buffered with a feedback loop. The amplified signal is directed across an output load resistor. 
     The analog HF-B signal from the optical head assembly  174  is taken from pins  17  and  16  of connector  155  ( FIGS. 22 and 23 ). As above, the signal is amplified and buffered. 
     The analog HF-C signal from the optical head assembly  174  is taken from pins  15  and  18  of connector  155  ( FIGS. 22 and 23 ). As above, the signal is amplified and buffered. 
     The analog HF-D signal from the optical head assembly  174  is taken from pins  13  and  20  of connector  155  ( FIGS. 22 and 23 ). As above, the signal is amplified and buffered. 
       FIG. 78B  is a partial electrical schematic of the buffer amplifier. Amplified signals HF-A, HF-B, HF-C, and HF-D pass through independent load resistors and are combined. The combined signal is fed into the negative input of an op amp, which is fed a variable positive signal. The amplified signal is buffered by a feedback loop, and directed across a variable load resistor before being fed into the negative input of another op amp. The amplified signal is buffered by a feedback loop and conditioned by an array of capacitors with a coil. The conditioned signal is then fed into the positive input of an op amp, which is buffered by a feedback loop. The amplified signal is then directed across an output load resistor and stabilization capacitor and is output at connector J 6  of output section  157  ( FIG. 22 ). 
     Optical Bio-Discs for Biological and Chemical Assays 
     The following discussion is directed to the biological and chemical applications for which the invention is useful. In sequencing applications, a sequence of nucleotide bases within the DNA sample can be determined by detecting which probes have the DNA sample bound thereto. In diagnostic applications, a genomic sample from an individual is screened against a predetermined set of probes to determine if the individual has a disease or a genetic disposition to a disease. 
     This invention combines microfluidic technology with genomics and proteomics on an optical bio-disc to detect investigational features in a test sample. Referring to  FIGS. 79A ,  79 B,  79 C, and  79 D, an aqueous test sample  252  is placed on or within an optical bio-disc  250  and is driven through micro-channels  254  across a specially prepared surface  256  to effectuate the desired tests. Capillary action, pressure applied with an external applicator, and/or centrifugal force (i.e., the force on a body in curvilinear motion directed away from the center or curvature or axis of rotation) act upon the test sample to achieve contact with capture probes  258 . Nucleic acid probe technology has application in detection of genetic mutations and related mechanisms, cancer screening, determining drug toxicity levels, detection of genetic disorders, detection of infectious disease, and genetic fingerprinting. 
     Additionally, the invention is adapted for use in a mixed phase system to perform hybridization assays. Referring to  FIGS. 80A ,  80 B,  80 C, and  80 D, a mixed phase assay involves performing hybridizations on a solid phase such as a thin nylon or nitrocellulose membrane  262 . For example, the assays usually involve spin-coating a thin layer of nitrocellulose  262  onto the substrate  264  of a bio-disc  260 , using a pipette  266  or similar device to load the membrane with a sample  268 , denaturing the DNA or creating single stranded molecules  270 , fixing the DNA or RNA to the membrane, and saturating the remaining membrane attachment sites with heterologous nucleic acids and/or proteins  272  to prevent the analytes and reporters from adhering to the membrane in a non-specific manner. All of these steps must be carried out before performing the actual hybridization. Subsequent steps are then performed to achieve hybridization and locate reporter beads in the capture areas or target zones. The incident beam is then utilized to detect the reporters as discussed in reference to  FIG. 79 . 
     Optical bio-discs are useful for experimental analysis and assays in the areas of genetics and proteomics in applications as diverse as pharmaco-genomics, gene expression, compound screening, toxicology, forensic investigation, Single Nucleotide Polymorphism (SNPs) analysis, Short Tandem Repeats (STRs), and clinical/molecular diagnostics. 
     Reporters 
     Many chemical, biochemical, and biological assays rely upon inducing a change in the optical properties of the particular sample being tested. Such a change may occur upon detection of the investigational feature itself (e.g., blood cells), or upon detection of a reporter. In the case where investigational features are too small to be detected by the read beam of the optical disc drive, reporters having a selective affinity (i.e., a tendency to react or combine with atoms or compounds of different chemical constitution for the investigational features within the test sample) for the investigational feature to facilitate detection. The reporter will react, combine, or otherwise bind to the investigational feature, thereby causing a detectable color, chemiluminescent, luminescent, or other identifiable label into the investigational feature. 
     Luminescence is formally divided into two categories, fluorescence and phosphorescence, depending on the nature of the excited state. A luminescent molecule has the ability to absorb photons of energy at one wavelength and subsequently emit the energy at another wavelength. Luminescence is caused by incident radiation impinging upon or exciting an electron of a molecule. The electron absorbs the incident radiation and is raised from a lower quantum energy level to a higher one. The excess energy is released as photons of light as the electron returns to the lower, ground-state energy level. Since each reporter has its own luminescent character, more than one labeled molecule, each tagged with a different reporter, can be used at the same time to detect two or more investigational features within the same test sample. 
     In addition to luminescence, techniques such as color staining using an enzyme-linked immunosorbent assay (ELISA) and gold labeling can be used to alter the optical properties of biological antigen material. For example, in order to test for the presence of an antibody in a blood sample, possibly indicating a viral infection, an ELISA can be carried out which produces a visible colored deposit if the antibody is present. Referring to  FIGS. 81A ,  81 B,  81 C,  81 D,  81 E, and  81 F, an ELISA makes use of a surface  280  that is coated with an antigen  282  specific to the antibody  284  to be tested for. Upon exposure of the surface to the blood sample  286 , antibodies in the sample bind to the antigens. Subsequent staining of the surface with specific enzyme-conjugated antibodies  288  and reaction of the enzyme with a substrate produces a precipitate  290  that correlates with the level of antigen binding and hence allows the presence of antibodies in the sample to be identified by the optical disc drive. This precipitate is then detected by the incident beam. Further details relating to use of precipitates as a reporting mechanism are disclosed in U.S. Provisional Application No. 60/292,110 entitled “Surface Assembly for Immobilizing DNA Capture Probes Using Pellets as Reporters in Genetic Assays Including Optical Bio-Discs and Methods Relating Thereto” filed May 18, 2001 and U.S. Provisional Application No. 60/313,917 entitled “Surface Assembly for Immobilizing DNA Capture Probes in Genetic Assays Using Enzymatic Reactions to Generate Signal in Optical Bio-Discs and Methods Relating Thereto” filed Aug. 21, 2001, both of which are herein incorporated by reference. 
     Referring to  FIG. 82 , bead-based assays involve use of spherical micro-particles, or beads  300  to alter the optical properties of biological antigen material  302 . The beads  300  are coated with a chemical layer  304  having a specific affinity for the investigational feature in a test sample. Referring to  FIGS. 83A ,  83 B,  83 C, and  83 D, when a test sample is loaded into or onto an optical disc  310  containing reporter beads  300  ( FIG. 82 ), the investigational feature  312 , if present, binds to the reporter beads  300 . Investigational feature  312  further binds to specific capture agents  314  on the surface  316  of the optical disc  310 . In this way, if the investigational feature is present in the biological solution, it becomes a binding agent to bind bead reporters  300  to capture agents  314  on the surface  316  of the bio-disc  310 . When the bio-disc is spun in the optical disc drive, the resulting centrifugal force sends unbound bead reporters  318  to an outer periphery of the disc, while bound bead reporters remain distributed over the area of the disc coated with the capture agent. The bound beads can be detected and quantified using an optical disc reader. Related dual bead assays are further disclosed in commonly assigned, co-pending U.S. patent application Ser. No. 09/997,741 entitled “Dual Bead Assays Including Optical Biodiscs and Methods Relating Thereto” filed Nov. 27, 2001, which is incorporated herein by reference. 
     Reporters useful in the invention include, but are not limited to, synthetic or biologically produced nucleic acid sequences, synthetic or biologically produced ligand-binding amino acids sequences, products of enzymatic reactions, and plastic micro-spheres or beads made of, for example, latex, polystyrene or colloidal gold particles with coatings of bio-molecules that have an affinity for a given material such as a biotin molecule in a strand of DNA. Appropriate coatings include those made from streptavidin or neutravidin, for example. These beads are selected in size so that the read or interrogation beam of the optical disc drive can “see” or detect a change of surface reflectivity caused by the particles. 
     In some embodiments associated with the present invention, reporter beads are bound to the disc surface through DNA hybridization. Referring to  FIGS. 84 and 85 , a capture probe  332  is attached to the disc surface  330 , while a signal probe  334  is attached to reporter beads  300  ( FIG. 82 ). In the case of a hybridization assay, both of the probes are complementary to the target sequence  336 . In the presence of target sequence  336 , both capture and signal probes hybridize with the target. In this manner, beads  300  are attached to disc surface  330 . In a subsequent centrifugation (or wash) step, all unbound beads are removed. Alternatively, the target itself is directly bound or linked to the beads without the presence of an extra signaling probe. 
     Alternatively, an investigational feature, if of adequate size for detection by the incident beam of an optical disc drive, may not require a reporter. Certain chemical reactions and the products and by-products resulting therefrom (i.e., precipitates), induce a sufficient change in the optical properties of the biological sample being tested. Such a change may also occur upon detection of the investigation feature itself, such as is the case when the invention is used to create an image of a microscopic structure. The optical disc drive detects changes in the optical properties of the surface of the bio-disc and creates images based thereon. 
     In a particular embodiment of the invention, an optical disc system (e.g.,  FIGS. 9A and 12 ) includes a signal processing system (e.g.,  142 , or  158  and  156 , or  158  and  32  with or without  154 , or  158  and  150  with or without  152  of  FIG. 9A ) and a photo detector circuit (e.g.,  18  of  FIG. 1 ) of an optical disc drive configured to generate at least one information-carrying signal (e.g., the HF, TE, or FE signals) from an optical disc assembly (e.g., disc  130  of  FIG. 12 ). The signal processing system is coupled to the photo detector  18  to obtain from the at least one information-carrying signal both operational information (e.g., tracking, focusing and speed signals of  FIG. 8 ) used to operate the optical disc system and indicia data (e.g., traces in  FIG. 61B ) indicative of a presence of an investigational feature (e.g., investigational feature  68  of  FIG. 43 ) associated with the optical disc assembly. 
     In a variant of the invention, the signal processing system of the optical disc system includes a PC and an analog-to-digital converter to provide a digitized signal to the PC. The analog-to-digital converter is coupled between the at least one information carrying signal and the PC. The PC includes a program module to detect and characterize peaks (e.g., see traces in  FIG. 61B ) in the digitized signal. Preferably, the PC further includes another program module to detect and count double peaks (e.g., see traces D and E in  FIG. 61B ) in the digitized signal. 
     In another variant of the invention, the signal processing system of the optical disc system includes a PC, an analog-to-digital converter to provide a digitized signal to the PC, and an analyzer  154  (implementation III of  FIG. 9A ) coupled between the analog-to-digital converter (e.g., the converter in  32  of  FIG. 8 ) and the PC. The analog-to-digital converter is coupled between the at least one information carrying signal and the PC. The analyzer includes logic to detect and characterize peaks in the digitized signal. Preferably, the analyzer further includes logic to detect and count double peaks in the digitized signal. 
     In still another variant of the invention, the signal processing system of the optical disc system includes a PC and an analog-to-digital converter to provide a digitized signal to the PC (implementation IV of  FIG. 9A ). The analog-to-digital converter is coupled between the at least one information carrying signal and the PC. The signal processing system further includes an audio processing module (e.g.,  156  of  FIG. 9A ) coupled between the at least one information-carrying signal and the analog-to-digital converter. Preferably, the optical disc assembly is pre-recorded with a predetermined sound, and the PC includes a program module to detect the indicia data in a deviation of the at least one information carrying signal from the predetermined sound when the investigational feature is present. In an alternative variant, the predetermined sound is encoded silence. 
     In still yet another variant of the invention, the signal processing system of the optical disc system includes a PC and an analog-to-digital converter to provide a digitized signal to the PC (implementation II of  FIG. 9A ). The analog-to-digital converter is coupled between the at least one information carrying signal and the PC. The signal processing system further includes an external buffer amplifier (e.g.,  152  of  FIG. 9A ) coupled between the at least one information-carrying signal and the analog-to-digital converter. 
     In a further variant of the invention, the signal processing system of the optical disc system includes a PC and an analog-to-digital converter to provide a digitized signal to the PC. The analog-to-digital converter is coupled between the at least one information carrying signal and the PC. The signal processing system further includes a trigger detection circuit (e.g.,  164  of  FIG. 12 ) coupled to the analog-to-digital converter. The trigger detection circuit is operative to detect a particular time in relation to a time when the indicia data is present in the at least one information-carrying signal. 
     In an alternative embodiment, the signal processing system includes a programmable digital signal processor selectively configurable to either (1) extract the operational information from the at least one information-carrying signal while in a first configuration or (2) operate as an analog-to-digital converter to provide the indicia data while in a second configuration. For example, see  FIG. 25  and implementation III of  FIG. 9A . 
     In another alternative embodiment, the signal processing system of the optical disc system includes a PC (e.g.,  158  of  FIG. 9A ), a programmable digital signal processor (e.g.,  32  of  FIG. 9A ) coupled to the at least one information-carrying signal, and an analyzer (e.g.,  154  of  FIG. 9A ) coupled between the programmable digital signal processor and the PC. The analyzer provides the indicia data as depicted in implementation III of  FIG. 9A . 
     In yet another alternative embodiment, the signal processing system of the optical disc system includes a trigger detection circuit (e.g.,  164  of  FIG. 12 ) that detects a time period during which the investigational feature associated with the optical disc assembly is scanned by the photo detector circuit. 
     In a further alternative embodiment, the signal processing system of the optical disc system includes a trigger detection circuit (e.g.,  164  of  FIG. 12 ) that detects a particular time in relation to a time when the indicia data is present in the at least one information-carrying signal. The time when the indicia data is present in the at least one information-carrying signal occurs periodically. The particular time is either (1) a predetermined time in advance of, (2) a time at, or (3) a predetermined time after each time the indicia data either begins to be present or ends in the at least one information-carrying signal. 
     In still yet another alternative embodiment, the signal processing system of the optical disc system includes a PC (e.g.,  158  of  FIG. 9A ), and an audio processing module (e.g.,  156  of  FIG. 9A ) coupled between the PC and the at least one information-carrying signal. Preferably, the sound processing module is either an external module independent of the optical disc drive, a drive module that is a part of the optical disc drive, or a modified drive module that is a part of the optical disc drive. In a variant of this embodiment, the PC includes a processor coupled to the sound module, and a software module stored in a memory to control the processor to extract the indicia data from sound data (e.g., see implementation IV of  FIG. 9A ). 
     In yet a further alternative embodiment, the photo detector circuit of the optical disc system includes circuitry to generate an analog signal as the at least one information-carrying signal. The analog signal includes either a high frequency signal from a photo detector, a tracking error signal, a focus error signal, an automatic gain control setting, a push-pull tracking signal, a CD tracking signal, a CD-R tracking signal, a focus signal, a differential phase detector signal, a laser power monitor signal or a sound signal. 
     In another embodiment, the optical disc system further includes the optical disc assembly (e.g.,  130  of  FIG. 12 ). The optical disc assembly has the associated investigational feature (e.g.,  136  of  FIG. 12 ) disposed on the assembly in a first disc sector and has the operational information (e.g.,  133  of  FIG. 12 ) used to operate the optical disc drive encoded on the assembly in a remaining disc sector. 
     In a variant, the optical disc assembly includes a trigger mark (e.g.,  166  of  FIG. 12 ) that is disposed on the optical disc assembly in a predetermined position relative to the first disc sector. The signal processing system further includes a trigger detection circuit (e.g.,  164  of  FIG. 12 ) that detects the trigger mark. Preferably, the trigger detection circuit detects the trigger mark periodically and detects the trigger mark either (1) a predetermined time in advance of, (2) a time at, or (3) a predetermined time after a time when the associated investigational feature is read by the photo detector circuit based on the predetermined position of the trigger mark relative to the first disc sector. 
     In a variant, the associated investigational feature of the optical disc assembly includes either plastic micro-spheres with a bio-molecule coating, colloidal gold beads with a bio-molecule coating, silica beads, glass beads, magnetic beads, or fluorescent beads. 
     In another embodiment of the invention, there is provided a method that includes the steps of depositing a test sample, spinning the optical disc, directing an incident beam, detecting a return beam, processing the detected return beam, and processing the detected return beam. The step of depositing a test sample includes depositing the sample at a predetermined location on an optical disc assembly. The step of spinning the optical disc includes spinning the assembly in an optical disc drive. The step of directing an incident beam includes directing the beam onto the optical disc assembly. The step of detecting a return beam includes detecting the return beam formed as a result of the incident beam interacting with the test sample. The step of processing the detected return beam processes the detected return beam to acquire information about an investigational feature associated with the test sample. 
     In a variant of this embodiment, the step of detecting a return beam forms a plurality of analog signals. The step of processing the detected return beam includes summing a first subset of the plurality of analog signals to produce a sum signal, combining either the first subset or a second subset of the plurality of analog signals to produce a tracking error signal, obtaining information used to operate an optical disc drive from the tracking error signal, and converting the sum signal to a digitized signal. 
     In another embodiment of the invention, the invention is a method that includes steps of acquiring a plurality of analog signals, summing a first subset, combining a second subset, obtaining information, and converting the sum signal to a digitized signal. The step of acquiring a plurality of analog signals acquires analog signals from an optical disc assembly using a plurality of photo detectors. The step of summing a first subset sums a first subset of the plurality of analog signals to produce a sum signal. The step of combining a second subset combines a second subset of the plurality of analog signals to produce a tracking error signal. The step of obtaining information obtains information used to operate an optical disc drive from the tracking error signal. 
     In a variant, the steps of acquiring and summing produce the sum signal that includes perturbations indicative of an investigational feature located at a location of the optical disc assembly. 
     In another variant, the method further includes a step of characterizing the investigational feature based on the digitized signal. 
     In another variant of the method, the step of converting includes configuring a portion of an optical disc drive chip set to operate as an analog-to-digital converter. Preferably, the step of configuring includes programming a digital signal processing chip within the optical disc drive chip set to operate as an analog-to-digital converter. Preferably, the digital signal processing chip includes a normalization function, an analog-to-digital converter function, a demodulation/decode function, and an output interface function. Preferably, the step of configuring further includes passing the sum signal around the demodulation/decode function by creating a path from the analog-to-digital converter function to the output interface function. Preferably, the step of configuring further includes deactivating the demodulation/decode function. 
     In another variant of the method, the step of converting includes configuring a digital signal processing chip that includes a normalization function, an analog-to-digital converter function, a demodulation/decode function, and an output interface function, and the step of configuring includes creating a path from the analog-to-digital converter function to the output interface function so that the sum signal is unprocessed by the demodulation/decode function. Preferably, the step of configuring includes deactivating the demodulation/decode function. 
     In yet another embodiment of the invention, a method includes steps of adapting a portion of a signal processing system, acquiring a plurality on analog signals, converting the analog signals, and characterizing investigational features based on a digitized signal. The step of adapting a portion of a signal processing system includes adapting the portion to operate as an analog-to-digital converter. The step of acquiring a plurality on analog signals acquires the analog signals from a photo detector circuit of an optical disc drive. The plurality of analog signals includes information that is indicative of investigational features on an optical disc assembly. The step of converting the analog signals converts the analog signals into a digitized signal with the signal processing system. Preferably, the step of adapting includes programming a digital signal processing chip within the signal processing system to operate as the analog-to-digital converter. 
     In another alternative embodiment of the invention, a method includes steps of receiving and converting. The step of receiving includes receiving each of at least one analog signal at a corresponding input of signal processing circuitry. The at least one analog signal has been provided by at least one corresponding photo detector element that detects light returned from a surface of an optical disc assembly. The step of converting includes converting each of the at least one analog signal into a corresponding digitized signal. Each digitized signal is substantially proportional to an intensity of the returned light detected by a corresponding one of the at least one photo detector element. 
     In a variant of this embodiment, the step of converting includes operating the signal processing circuitry to bypass any demodulation of a first digitized signal. Preferably, the step of converting further includes operating the signal processing circuitry to bypass any decoding of the first digitized signal, and operating the signal processing circuitry to bypass any checking for errors in the first digitized signal. 
     In another variant of this embodiment, the step of converting includes operating the signal processing circuitry to bypass any decoding of a first digitized signal. 
     In yet another variant of this embodiment, the step of converting includes operating the signal processing circuitry to bypass any checking for errors in a first digitized signal. 
     In still another variant of this embodiment, the method further includes a step of combining at least two of the at least one analog signal. Preferably, the step of combining is a step selected from a group consisting of adding, subtracting, dividing, multiplying, and a combination thereof. Preferably, the step of combining is performed before the step of converting. Alternatively, the step of combining may be performed after the step of converting. 
     In a further variant, the method further includes a step of supplying a first digitized signal of the at least one digitized signal at an output interface of the signal processing circuitry after the step of converting without substantially modifying the first digitized signal between the steps of converting and supplying. Preferably, the signal processing circuitry includes a digital signal processor. Preferably, the signal processing circuitry consists of a digital signal processor. 
     The materials for use in the method of the invention are ideally suited for the preparation of a kit. Such a kit may include a carrier member being compartmentalized to receive in close confinement an optical bio-disc and one or more containers such as vials, tubes, and the like, each of the containers including a separate element to be used in the method. For example, one of the containers may include a reporter and/or protein-specific binding reagent, such as an antibody. Another container may include isolated nucleic acids, antibodies, proteins, and/or reagents described herein, known in the art or developed in the future. The constituents may be present in liquid or lyophilized form, as desired. The antibodies used in the assay kits of the present invention may be monoclonal or polyclonal antibodies. For convenience, one may also provide the reporter affixed to the substrate of the bio-disc. Additionally, the reporters may further be combined with an indicator, (e.g., a radioactive label or an enzyme) useful in assays developed in the future. A typical kit also includes a set of instructions for any or all of the methods described herein. 
     In a variant of this embodiment, the carrier may be further compartmentalized to include a setup optical disc containing software for configuring a computer for use with the bio-disc. Optionally, the kit may be packaged with a modified optical disc drive. For example, the kit may be sold for educational purposes as an alternative to the common microscope. 
     While this invention has been described in detail with reference to a certain preferred embodiments, it should be appreciated that the present invention is not limited to those precise embodiments. Rather, in view of the present disclosure, which describes the current best mode for practicing the invention, many modifications and variations would present themselves to those of skill in the art without departing from the scope and spirit of this invention. The scope of the invention is, therefore, indicated by the following claims rather than by the foregoing description. All changes, modifications, and variations coming within the meaning and range of equivalency of the claims are to be considered within their scope. 
     Having thus described the invention with the details and particularity required by the patent laws, what is claimed and desired protected by Letters Patent is set forth in the appended claims.