Patent Publication Number: US-7222025-B2

Title: System, method, and product for dynamic noise reduction in scanning of biological material

Description:
RELATED APPLICATIONS 
     This application is a continuation of U.S. application Ser. No. 10/304,092 filed Nov. 25, 2002, now U.S. Pat. No. 6,813,567 which is a continuation of U.S. application Ser. No. 09/683,216 filed 09/683,216 filed Dec. 3, 2001, now U.S. Pat. No. 6,490,533 issued Dec. 3, 2002 which claims priority from U.S. Provisional Patent Application Ser. No. 60/286,578, filed Apr. 26, 2001. The entire disclosure and contents of the above patents and applications are hereby incorporated by reference. The present application is related to a U.S. patent application entitled “System, Method, and Product for Pixel Clocking in Scanning of Biological Materials,” and to a U.S. patent application entitled “System, Method, and Product for Symmetrical Filtering in Scanning of Biological Materials,” both of which are filed concurrently herewith and both of which are hereby incorporated by reference herein in their entireties for all purposes. 
    
    
     BACKGROUND 
     1. Field of the Invention 
     The present invention relates to scanning systems for examining biological material and, in particular, to noise reduction in optical scanning systems having a laser to excite fluorescently tagged biological materials. 
     2. Related Art 
     Synthesized nucleic acid probe arrays, such as Affymetrix® GeneChip® synthesized probe arrays, have been used to generate unprecedented amounts of information about biological systems. For example, a commercially available GeneChip® array set from Affymetrix, Inc. of Santa Clara, Calif., is capable of monitoring the expression levels of approximately 6,500 murine genes and expressed sequence tags (EST&#39;s). Experimenters can quickly design follow-on experiments with respect to genes, EST&#39;s, or other biological materials of interest by, for example, producing in their own laboratories microscope slides containing dense arrays of probes using the Affymetrix® 417™ or 427™ Arrayers or other spotting devices. Analysis of data from experiments with synthesized and/or spotted probe arrays may lead to the development of new drugs and new diagnostic tools. 
     In some conventional applications, this analysis begins with the capture of fluorescent signals indicating hybridization of labeled target samples with probes on synthesized or spotted probe arrays. The devices used to capture these signals often are referred to as scanners. Due to the relatively small emission signals sometimes available from the hybridized target-probe pairs, the presence of background fluorescent signals, the high density of the arrays, variations in the responsiveness of various fluorescent labels, and other factors, care must be taken in designing scanners to properly acquire and process the fluorescent signals indicating hybridization. For example, U.S. Pat. No. 6,171,793 to Phillips, et al., hereby incorporated herein in its entirety for all purposes, describes a method for scanning probe arrays to provide data having a dynamic range that exceeds that of the scanner. Nonetheless, there is a continuing need to improve scanner design to provide more accurate and reliable fluorescent signals and thus provide experimenters with more sensitive and accurate data. 
     SUMMARY OF THE INVENTION 
     Systems, methods, and products to address these and other needs are described herein with respect to illustrative, non-limiting, implementations. Various alternatives, modifications and equivalents are possible. For example, certain systems, methods, and computer software products are described herein using exemplary implementations for analyzing data from arrays of biological materials produced by the Affymetrix® 417™ or 427™ Arrayer. Other illustrative implementations are referred to in relation to data from Affymetrix® GeneChip® probe arrays. However, these systems, methods, and products may be applied with respect to many other types of probe arrays and, more generally, with respect to numerous parallel biological assays produced in accordance with other conventional technologies and/or produced in accordance with techniques that may be developed in the future. For example, the systems, methods, and products described herein may be applied to parallel assays of nucleic acids, PCR products generated from cDNA clones, proteins, antibodies, or many other biological materials. These materials may be disposed on slides (as typically used for spotted arrays), on substrates employed for GeneChip® arrays, or on beads, optical fibers, or other substrates or media. Moreover, the probes need not be immobilized in or on a substrate, and, if immobilized, need not be disposed in regular patterns or arrays. For convenience, the term “probe array” will generally be used broadly hereafter to refer to all of these types of arrays and parallel biological assays. 
     In accordance with one preferred embodiment, a method is described that includes the steps of (1) directing an excitation beam to a plurality of pixel locations on a substrate; (2) determining one or more representative excitation values, each related to a value of the excitation beam as directed to at least one of the plurality of pixel locations; (3) detecting an emission signal having one or more emission values; (4) correlating each of the one or more emission values with one or more of the representative excitation values; (5) providing at least one excitation reference value; (6) comparing the excitation reference value to at least one representative excitation value, thereby generating a normalization factor; and (7) adjusting at least one emission value based, at least in part, on the normalization factor. One or more probes of a biological microarray may be disposed in relation to the substrate; for example, probes may be coupled to the substrate. The one or more probes may be disposed at different probe locations on a surface of the substrate. In some implementations, the substrate may include different polymer sequences coupled to the surface of the substrate. The different polymer sequences may include different oligonucleotide sequences, wherein each of the different polymer sequences is coupled in a different probe location of the surface. In some implementations, each of the probe locations has an area of one-hundredth of a square centimeter or less. Also, in some implementations, the substrate may include more than one thousand different ligands of known sequence collectively occupying an area of less than one square centimeter, the different ligands occupying different known locations within the area. 
     In accordance with further implementations of these preferred embodiments, step (2) includes directing the excitation beam to a dichroic mirror, and determining the representative excitation values based on a partial excitation beam that passes through the dichroic mirror. Also, the emission signal may arise from the direction of the excitation beam to the plurality of pixel locations. As used in this context, the word “arise” is intended to have a broad meaning so as to encompass various cause and effect relationships wherein the directing of the excitation beam causes or results in, directly or indirectly, the emission signal. As just one non-limiting example, the excitation beam may be a laser beam directed to a location on the substrate where fluorescently labeled receptors are disposed, and the emission signal may be a fluorescent signal resulting from excitation of those labeled receptors. In these and other implementations, step (4) may include spatially correlating the emission values with the representative excitation values. Also in these and other implementations, step (2) may include determining a first representative excitation value related to a power of the excitation beam as directed to a first of the plurality of pixel locations; step (3) may include detecting an emission value arising from the direction of the excitation beam to the first pixel location; and step (4) may include correlating the first emission value with the first representative excitation value. In accordance with various embodiments, the excitation reference value may be based, at least in part, on at least one of the one or more representative excitation values, and/or on a plurality of representative excitation values related to values of the excitation beam as directed to pixel locations in one or more scan lines. 
     The method, in accordance with some embodiments, may further include the step of (8) filtering the representative excitation values to provide one or more filtered representative excitation values. In these embodiments, the excitation reference value is based, at least in part, on at least one of the one or more filtered representative excitation values. In these and other embodiments, the excitation reference value may be based, at least in part, on a measured calibration value and/or on a predetermined specification value. 
     In accordance with yet other embodiments, a system is described for processing an emission signal having one or more emission values. The system includes an excitation signal generator that provides an excitation signal having one or more representative excitation values representative of an excitation beam. The system also has an excitation reference provider that provides at least one excitation reference value; a normalization factor generator that compares the excitation reference value to at least one representative excitation value, thereby generating a normalization factor; and a comparison processor that adjusts at least one emission value corresponding to the at least one representative excitation value based, at least in part, on the normalization factor. The excitation reference value may be determined based at least in part on a low-frequency component of the excitation signal. The at least one representative excitation value may include, as examples, an instantaneous analog value or a sampled digital value. In some implementations, the comparison processor adjusts the at least one emission value corresponding to the at least one representative excitation value based on multiplying or dividing the emission value by the normalization factor. The excitation signal may include a laser signal, and the emission signal may include a fluorescent signal resulting from excitation of a fluorophore by the laser signal. 
     In accordance with a further embodiment, a method is described for processing an emission signal having one or more emission values. The method includes providing at least one excitation reference value; comparing the excitation reference value to at least one excitation value, thereby generating a normalization factor; and adjusting at least one emission value corresponding to the at least one excitation value based, at least in part, on the normalization factor. 
     A scanning system is described in accordance with some embodiments. The system includes one or more excitation sources that generate one or more excitation beams; an excitation signal generator that provides an excitation signal having one or more representative excitation values representative of the excitation beam; an excitation reference provider that provides at least one excitation reference value; a normalization factor generator that compares the excitation reference value to at least one representative excitation value, thereby generating a normalization factor; and a comparison processor that adjusts at least one emission value corresponding to the at least one representative excitation value based, at least in part, on the normalization factor. The scanning system may include a processor and a memory unit, wherein the normalization factor generator includes a set of normalization factor generating instructions stored in the memory unit and executed in cooperation with the processor. The comparison processor may also include a set of comparison processing instructions stored in the memory unit and executed in cooperation with the processor. 
     A computer program product is described with respect to other embodiments. The product includes a set of normalization factor generating instructions stored in a memory unit of a computer and executed in cooperation with a processor of the computer. These instructions are constructed and arranged to compare at least one excitation reference value to at least one representative excitation value, thereby generating a normalization factor. The product also includes a set of comparison processing instructions stored in the memory unit and executed in cooperation with the processor, constructed and arranged to adjust at least one emission value corresponding to the at least one representative excitation value based, at least in part, on the normalization factor. The at least one emission value results from excitation of a labeled receptor at a probe location of a probe array. 
     A method for analyzing molecules is described with respect to some embodiments. The method includes (1) directing an excitation beam to a plurality of pixel locations on a surface having a plurality of probe locations, each probe location including one or more probe molecules; (2) determining one or more representative excitation values, each related to a value of the excitation beam as directed to at least one of the plurality of pixel locations; (3) detecting an emission signal having one or more emission values; (4) correlating each of the one or more emission values with one or more of the representative excitation values; (5) providing at least one excitation reference value; (6) comparing the excitation reference value to at least one representative excitation value, thereby generating a normalization factor; (7) adjusting at least one emission value based, at least in part, on the normalization factor; and (8) analyzing at least one probe location based, at least in part, on the at least one adjusted emission value. 
     The above embodiments and implementations are not necessarily inclusive or exclusive of each other and may be combined in any manner that is non-conflicting and otherwise possible, whether they be presented in association with a same, or a different, embodiment or implementation. The description of one embodiment or implementation is not intended to be limiting with respect to other embodiments and/or implementations. Also, any one or more function, step, operation, or technique described elsewhere in this specification may, in alternative implementations, be combined with any one or more function, step, operation, or technique described in the summary. Thus, the above embodiment and implementations are illustrative rather than limiting. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The above and further features will be more clearly appreciated from the following detailed description when taken in conjunction with the accompanying drawings. In the drawings, like reference numerals indicate like structures or method steps and the leftmost digit of a reference numeral indicates the number of the figure in which the referenced element first appears (for example, the element  160  appears first in  FIG. 1 ). In functional block diagrams, rectangles generally indicate functional elements and parallelograms generally indicate data. In method flow charts, rectangles generally indicate method steps and diamond shapes generally indicate decision elements. All of these conventions, however, are intended to be typical or illustrative, rather than limiting. 
         FIG. 1  is a simplified graphical representation of an arrangement of scanner optics and detectors suitable for providing excitation and emission signals for processing by a noise compensation module such as shown in  FIG. 4  or  9 ; 
         FIG. 2A  is a perspective view of a simplified exemplary configuration of a scanning arm portion of the scanner optics and detectors of  FIG. 1 ; 
         FIG. 2B  is a top planar view of the scanning arm of  FIG. 2A  as it scans biological features on one embodiment of a probe array being moved by a translation stage under the arm&#39;s arcuate path; 
         FIG. 3  is a functional block diagram of one embodiment of a scanner-computer system including a scanner having a noise compensation module such as shown in  FIG. 4  or  9 ; 
         FIG. 4  is a functional block diagram of one embodiment of a noise compensation module for providing an emission signal normalized to compensate for noise in the excitation source; 
         FIG. 5A  is a graphical representation of one embodiment of a probe feature showing bi-directional scanning lines such as may be implemented using the scanning arm of  FIGS. 2A and 2B ; 
         FIG. 5B  is an illustrative plot of pixel clock pulses aligned with the scanned probe feature of  FIG. 5A  to show illustrative radial position sampling points; 
         FIG. 5C  is an illustrative plot of sampled emission voltages aligned with the pixel clock pulses of  FIG. 5B ; 
         FIG. 5D  is an illustrative plot of sampled excitation voltages aligned with the pixel clock pulses of  FIG. 5B ; 
         FIG. 6A  is a graphical representation of a simulated input waveform including noise; 
         FIGS. 6B and 6C  are graphical representations of output waveforms from alternative embodiments of asymmetrical filters responsive to the input waveform of  FIG. 6A ; 
         FIGS. 6D and 6E  are graphical representations of output waveforms from alternative embodiments of symmetrical filters responsive to the input waveform of  FIG. 6A ; 
         FIG. 7A  is a graphical representation of an input waveform plotted as a function of pixel clock pulses; 
         FIG. 7B  is a graphical representation of an output waveform from one embodiment of an asymmetrical filter responsive to the input waveform of  FIG. 7A  as a function of pixel clock pulses in a sequence determined by scanning in a first direction; 
         FIG. 7C  is a graphical representation of an output waveform from the asymmetrical filter of  FIG. 7B  responsive to the input waveform of  FIG. 7A  as a function of pixel clock pulses in a sequence determined by scanning in a second direction opposite to the first direction; 
         FIG. 7D  is a consolidated graphical representation of pixels shown in  FIGS. 7B and 7C  resulting from successive bi-directional scans of a probe feature under asymmetrical filtering; 
         FIG. 7E  is a graphical representation of the pixels of  FIG. 7D  shifted so as to graphically compensate for the effects of phase delay; 
         FIG. 8A  is a graphical representation of an input waveform plotted as a function of pixel clock pulses; 
         FIG. 8B  is a graphical representation of an output waveform from one embodiment of a symmetrical filter responsive to the input waveform of  FIG. 8A  as a function of pixel clock pulses in a sequence determined by scanning in a first direction; 
         FIG. 8C  is a graphical representation of an output waveform from the symmetrical filter of  FIG. 8B  responsive to the input waveform of  FIG. 8A  as a function of pixel clock pulses in a sequence determined by scanning in a second direction opposite to the first direction; 
         FIG. 8D  is a consolidated graphical representation of pixels shown in  FIGS. 8B and 8C  resulting from successive bidirectional scans of a probe feature under symmetrical filtering; 
         FIG. 8E  is a graphical representation of the pixels of  FIG. 8D  shifted so as to graphically compensate for the effects of phase delay; 
         FIG. 9  is a functional block diagram of one embodiment of a noise compensation module for providing, together with a digital signal processing board and software on an associated computer, emission data normalized to compensate for noise in the excitation source; and 
         FIG. 10  is a functional block diagram of one embodiment of aspects of a computer of the scanner-computer system of  FIG. 3  suitable for generating normalized emission signal data. 
     
    
    
     DETAILED DESCRIPTION 
     The description below is designed to present preferred embodiments and not to be construed as limiting in any way. Also, reference will be made to articles and patents to show general features that are incorporated into the present disclosure. Many scanner designs may be used in order to provide excitation and emission signals appropriate for processing by noise compensation module  310 , which is described in detail below. In reference to the illustrative implementation of  FIG. 1 , the term “excitation beam” refers to light beams generated by lasers. However, excitation sources other than lasers may be used in alternative implementations. Thus, the term “excitation beam” is used broadly herein. The term “emission beam” also is used broadly herein. A variety of conventional scanners detect fluorescent or other emissions from labeled target molecules or other material associated with biological probes. Other conventional scanners detect transmitted, reflected, or scattered radiation from such targets. These processes are sometimes generally and collectively referred to hereafter for convenience simply as involving the detection of “emission beams.” Various detection schemes are employed depending on the type of emissions and other factors. A typical scheme employs optical and other elements to provide an excitation beam, such as from a laser, and to selectively collect the emission beams. Also generally included are various light-detector systems employing photodiodes, charge-coupled devices, photomultiplier tubes, or similar devices to register the collected emission beams. For example, a scanning system for use with a fluorescently labeled target is described in U.S. Pat. Nos. 5,143,854 and 6,225,625, hereby incorporated by reference in their entireties for all purposes. Other scanners or scanning systems are described in U.S. Pat. Nos. 5,578,832; 5,631,734; 5,834,758; 5,936,324; 5,981,956; 6,025,601; 6,141,096; 6,185,030; 6,201,639; and 6,218,803 and in PCT Application PCT/US99/06097 (published as WO99/47964), each of which also is hereby incorporated by reference in its entirety for all purposes. 
     Scanner Optics and Detectors  100 . 
       FIG. 1  is a simplified graphical representation of illustrative scanner optics and detectors (hereafter, simply “scanner optics”)  100 . Scanner optics  100  includes excitation sources  120 A and  120 B (generally and collectively referred to as excitation sources  120 ). Any number of one or more excitation sources  120  may be used in alternative embodiments. In the present example, sources  120  are lasers; in particular, source  120 A is a diode laser producing red laser light having a wavelength of 635 nanometers and, source  120 B is a doubled YAG laser producing green laser light having a wavelength of 532 nanometers. Further references herein to sources  120  generally will assume for illustrative purposes that they are lasers, but, as noted, other types of sources, e.g., x-ray sources, may be used in other implementations. 
     In the illustrated implementation, it is assumed that only one of excitation sources  120 A and  120 B is operational (in the sense of generating an excitation beam  135 ) at any particular time. For example, source  120 A and not source  120 B may be operational for one arc scan by scanner optics  100 , as described below, and source  120 B and not source  120 A may be operational for a subsequent scan. Sources  120 A and  120 B may alternate between successive scans, groups of successive scans, or between full scans of an array. For clarity, excitation beams  135 A and  135 B are shown as distinct from each other in  FIG. 1 . However, in practice, turning mirror  124  and/or other optical elements (not shown) typically are adjusted to provide that these beams follow the same path. Moreover, it also will be understood that the assumption that only one laser is operational at a time is made only for the sake of convenience and clarity of illustration. Implementations are contemplated that include simultaneous operation of any number of excitation sources  120 . Beams  135  in simultaneous operation typically, but need not, follow the same path.  Handbook of Biological Confocal Microscopy  (James B. Pawley, ed.) (2.ed.; 1995; Plenum Press, NY), which includes information known to those of ordinary skill in the art regarding the use of lasers and associated optics, is hereby incorporated herein by reference in its entirety. 
     Scanner optics  100  also includes excitation filters  125 A and  125 B that optically filter beams from excitation sources  120 A and  120 B, respectively. Filters  125  optionally are used to remove light at wavelengths other than the desired wavelengths, and need not be included if, for example, sources  120 A and  120 B do not produce light at these extraneous wavelengths. As noted, however, it may be desirable in some applications to use inexpensive lasers and often it is cheaper to filter out-of-mode laser emissions than to design the laser to avoid producing such extraneous emissions. 
     The filtered excitation beams from sources  120 A and  120 B are combined in accordance with any of a variety of known techniques. For example, one or more mirrors, such as turning mirror  124 , may be used to direct filtered beam from source  120 A through beam combiner  130 . The filtered beam from source  120 B is directed at an angle incident upon beam combiner  130  such that the beams combine in accordance with optical properties techniques well known to those of ordinary skill in the relevant art. Most of combined excitation beams  135 A and  135 B (generally and collectively referred to as beams  135 ) are reflected by dichroic mirror  136  and thence directed to periscope mirror  138  of the illustrative example. However, dichroic mirror  136  has characteristics selected so that portions of beams  135 A and  135 B, referred to respectively as partial excitation beams  137 A and  137 B and generally and collectively as beams  137 , pass through it so that they may be detected by excitation detector  110 . 
     Detector  110  may be any of a variety of conventional devices for detecting partial excitation beams  137 , such as a silicon detector for providing an electrical signal representative of detected light, a photodiode, a charge-coupled device, a photomultiplier tube, or any other detection device for providing a signal indicative of detected light that is now available or that may be developed in the future. Detector  110  generates excitation signal  194  that represents detected partial excitation beams  137 A or  137 B. In accordance with known techniques, the amplitude, phase, or other characteristic of excitation signal  194  is designed to vary in a known or determinable fashion depending on the power of excitation beam  135 . The term “power” in this context refers to the capability of beam  135  to evoke emissions. For example, the power of beam  135  typically may be measured in milliwatts of laser energy with respect to the illustrated example in which the laser energy evokes a fluorescent signal. Thus, excitation signal  194  has values that represent the power of beam  135  during particular times or time periods. 
     In the illustrated example, excitation beams  135  are directed via periscope mirror  138  and arm end turning mirror  142  to an objective lens  145 . As described in greater detail below in relation to  FIGS. 2A and 2B , lens  145  in the illustrated implementation is a small, light-weight lens located on the end of an arm that is driven by a galvanometer around an axis perpendicular to the plane represented by galvo rotation  149  shown in  FIG. 1 . Objective lens  145  thus moves in arcs over a substrate upon which biological materials have been synthesized or have been deposited. Flourophores associated with these biological materials emit emission beam  152  (beam  152 A in response to excitation beam  135 A, and beam  152 B in response to excitation beam  135 B) at characteristic wavelengths in accordance with well known principles. Emission beam  152  in the illustrated example follows the reverse path as described with respect to excitation beam  135  until reaching dichroic mirror  136 . In accordance with well known techniques and principles, the characteristics of mirror  136  are selected so that beam  152  (or a portion of it) passes through the mirror rather than being reflected. 
     In the illustrated implementation, filter wheel  160  is provided to filter out spectral components of emission beam  152  that are outside of the emission band of the fluorophore. The emission band is determined by the characteristic emission frequencies of those fluorophores that are responsive to the frequency of excitation beam  135 . Thus, for example, excitation beam  135 A from source  120 A, which is illustratively assumed to have a wavelength of 635 nanometers, excites certain fluorophores to a much greater degree than others. The characteristic emission wavelength of a first illustrative fluorophore (not shown in  FIG. 1 ) when excited by beam  135 A is assumed to be 665 nanometers. Emission beam  152 A in this example typically will also include wavelengths above and below 665 nanometers in accordance with distributions that are known to those of ordinary skill in the relevant art. Similarly, the characteristic emission wavelength of a second illustrative fluorophore (not shown in  FIG. 1 ), when excited by beam  135 A having a wavelength of 532 nanometers, is illustratively assumed to be 551 nanometers. Thus, when excitation source  120 A is operational, filter wheel  160  is turned so that filter  162 A is selected (typically under computer control) and wavelengths other than 665 nanometers are removed from filtered emission beam  154 . Similarly, filter  162 B is selected when source  120 B is operational so that wavelengths other than 551 nanometers are filtered out of beam  152 B to produce filtered emission beam  154 . In accordance with techniques well known to those of ordinary skill in the relevant arts, including that of confocal microscopy, beam  154  may be focused by various optical elements such as lens  165  and also passed through illustrative pinhole  167  or other element to limit the depth of field, and thence impinges upon emission detector  115 . 
     Similar to excitation detector  110 , emission detector  115  may be a silicon detector for providing an electrical signal representative of detected light, or it may be a photodiode, a charge-coupled device, a photomultiplier tube, or any other detection device that is now available or that may be developed in the future for providing a signal indicative of detected light. Detector  115  generates emission signal  192  that represents filtered emission beam  154  in the manner noted above with respect to the generation of excitation signal  194  by detector  110 . Emission signal  192  and excitation signal  194  are provided to noise compensation module  310  for processing, as described below in relation to  FIGS. 3 and 4 . 
       FIG. 2A  is a perspective view of a simplified representation of an illustrative scanning arm portion of scanner optics  100  in accordance with this particular, non-limiting, implementation. Arm  200  moves in arcs around axis  210 , which is perpendicular to the plane of galvo rotation  149 . A position transducer  215  is associated with galvanometer  215  that, in the illustrated implementation, moves arm  200  in bi-directional arcs. Transducer  215 , in accordance with any of a variety of known techniques, provides an electrical signal indicative of the radial position of arm  200 . Certain non-limiting implementations of position transducers for galvanometer-driven scanners are described in U.S. Pat. No. 6,218,803 to Montagu, et al., which is hereby incorporated by reference in its entirety for all purposes. As described below, the signal from transducer  215  is provided in the illustrated implementation to computer  350  so that clock pulses may be provided for digital sampling of emission signals when arm  200  is in certain positions along its scanning arc. 
     Arm  200  is shown in alternative positions  200 ′ and  200 ″ as it moves back and forth in scanning arcs about axis  210 . Excitation beams  135  pass through objective lens  145  on the end of arm  200  and excite fluorophores that may be contained in hybridized probe-target pairs in features  230  on a substrate of probe array  240 , as further described below. The arcuate path of excitation beams  135  over probe array  240  is schematically shown for illustrative purposes as path  250 . Emission beams  152  pass up through objective lens  145  as noted above. Probe array  240  of this example is disposed on translation stage  242  that is moved in direction  244  so that arcuate path  250  repeatedly crosses the plane of probe array  240 . As is evident, the resulting coverage of excitation beams  135  over the plane of probe array  240  is therefore determined by the footprint of beam, the speed of movement in direction  244 , and the speed of the scan.  FIG. 2B  is a top planar view of arm  200  with objective lens  145  scanning features  230  on probe array  240  as translation stage  242  is moved under path  250 . As shown in  FIG. 2B , arcuate path  250  of this example is such that arm  200  has a radial displacement of 0 in each direction from an axis parallel to direction  244 . For convenience of reference below, a direction  243  perpendicular to direction  244  is also shown in  FIG. 2B . For illustrative purposes, direction  243  may hereafter be referred to as the “x” direction, and direction  244  as the “y” direction. 
     Further details of confocal, galvanometer-driven, arcuate, laser scanning instruments suitable for detecting fluorescent emissions are provided in PCT Application PCT/US99/06097 (published as WO99/47964) and in U.S. Pat. Nos. 6,185,030; 6,201,639; and 6,225,625, all of which have been incorporated by reference above. 
     Probe Array  240 . 
     Probe array  240  as shown in  FIGS. 2A and 2B  is illustrative only and it will be understood that numerous variations are possible with respect to providing biological materials for scanning. For example, Affymetrix® GeneChip® arrays commercially available from Affymetrix, Inc., of Santa Clara, Calif., referred to above, are synthesized in accordance with techniques sometimes referred to as VLSIPS™ (Very Large Scale Immobilized Polymer Synthesis) technologies. Probe arrays developed with these technologies, and others that are now available and may in the future be developed for synthesizing arrays of biological materials, may hereafter be referred to for convenience as “synthesized probe arrays.” This term refers generally to arrays in which probes have been built in situ on an array substrate, as contrasted, for example, to arrays in which pre-synthesized or pre-selected probes are deposited or positioned on or within a substrate. 
     Some aspects of VLSIPS™ technologies are described in the following U.S. Pat. No. 5,143,854 to Pirrung, et al.; U.S. Pat. No. 5,445,934 to Fodor, et al.; U.S. Pat. No. 5,744,305 to Fodor, et al.; U.S. Pat. No. 5,831,070 to Pease, et al.; U.S. Pat. No. 5,837,832 to Chee, et al.; U.S. Pat. No. 6,022,963 to McGall, et al.; and U.S. Pat. No. 6,083,697 to Beecher, et al. Each of these patents is hereby incorporated by reference in its entirety. The probes of these arrays typically consist of oligonucleotides that typically are synthesized by methods that include the steps of activating regions of a substrate and then contacting the substrate with a selected monomer solution. The regions are activated with a light source shown through a mask in a manner similar to photolithographic techniques used in the fabrication of integrated circuits. Other regions of the substrate remain inactive because the mask blocks them from illumination. By repeatedly activating different sets of regions and contacting different monomer solutions with the substrate, a diverse array of polymers is produced on the substrate. A variety of other techniques also exist for synthesizing probe arrays. For example, U.S. Pat. Nos. 5,885,837 and 6,040,193 describe the use of micro-channels or micro-grooves on a substrate, or on a block placed on a substrate, to synthesize arrays of biological materials. 
     As noted, techniques also exist for depositing or positioning pre-synthesized or pre-selected probes on or within a substrate or support. For convenience, probe arrays made in accordance with these other techniques, or depositing/positioning techniques that may be developed in the future, may hereafter be referred to as “spotted arrays.” Typically, spotted arrays are commercially fabricated on microscope slides. These arrays typically consist of liquid spots containing biological material of potentially varying compositions and concentrations. For instance, a spot in the array may include a few strands of short polymers, such as oligonucleotides in a water solution, or it may include a high concentration of long strands of polymers, such as complex proteins. The Affymetrix® 417™ and 427™ Arrayers are devices that deposit densely packed probe arrays of biological material on a microscope slide in accordance with these techniques. Aspects of these, and other, spot arrayers are described in U.S. Pat. Nos. 6,121,048 and 6,136,269, in PCT Applications Nos. PCT/US99/00730 (International Publication Number WO99/36760) and PCT/US 01/04285, in U.S. patent application Ser. Nos. 09/122,216, 09/501,099, and 09/862,177, and in U.S. Provisional Patent Application Ser. No. 60/288,403, all of which are hereby incorporated by reference in their entireties for all purposes. Other techniques for generating spotted arrays also exist. For example, U.S. Pat. No. 6,040,193 to Winkler, et al. is directed to processes for dispensing drops to generate spotted arrays. The &#39;193 patent, and U.S. Pat. No. 5,885,837 to Winkler, also describe separating reactive regions of a substrate from each other by inert regions and spotting on the reactive regions. The &#39;193 and &#39;837 patents are hereby incorporated by reference in their entireties. Other techniques are based on ejecting jets of biological material to form spotted arrays. Other implementations of the jetting technique may use devices such as syringes or piezo electric pumps to propel the biological material. 
     Synthesized or spotted probe arrays typically are used in conjunction with tagged biological samples such as cells, proteins, genes or EST&#39;s, other DNA sequences, or other biological elements. These samples, referred to herein as “targets,” are processed so that they are spatially associated with certain probes in the probe array. For example, one or more chemically tagged biological samples, i.e., the targets, are distributed over the probe array. Some targets hybridize with at least partially complementary probes and remain at the probe locations, while non-hybridized targets are washed away. These hybridized targets, with their “tags” or “labels,” are thus spatially associated with the targets&#39; complementary probes. The hybridized probe and target may sometimes be referred to as a “probe-target pair.” Detection of these pairs by scanners can serve a variety of purposes, such as to determine whether a target nucleic acid has a nucleotide sequence identical to or different from a specific reference sequence. See, for example, U.S. Pat. No. 5,837,832, referred to and incorporated above. Other uses include gene expression monitoring and evaluation (see, e.g., U.S. Pat. No. 5,800,992 to Fodor, et al.; U.S. Pat. No. 6,040,138 to Lockhart, et al.; and International App. No. PCT/US98/15151, published as WO99/05323, to Balaban, et al.), genotyping (U.S. Pat. No. 5,856,092 to Dale, et al.), or other detection of nucleic acids. The &#39;992, &#39;138, and &#39;092 patents, and publication WO99/05323, are incorporated by reference herein in their entirety for all purposes for the uses stated above and all the uses that are disclosed therein. 
     To ensure proper interpretation of the term “probe” as used herein, it is noted that contradictory conventions exist in the relevant literature. The word “probe” is used elsewhere in some contexts to refer not to the biological material that is synthesized on a substrate or deposited on a slide, as described above, but to what has been referred to herein as the “target.” To avoid confusion, the term “probe” is used herein to refer to probes such as those synthesized according to the VLSIPS™ technology; the biological materials deposited or positioned so as to create spotted arrays; and materials synthesized, deposited, or positioned to form arrays according to other current or future technologies. Moreover, as noted, the term “probe” is not limited to probes immobilized in array format. Rather, the functions and methods described herein may also be employed with respect to other parallel assay devices and techniques. Also, in some cases the sequence and/or composition of the probes may not be known, or may not be fully known. 
     Noise Compensation Module  310 . 
       FIG. 3  is a functional block diagram of a scanner-computer system showing scanner  300  under the control of computer  350 . A component of scanner  300  is noise compensation module  310  that, among other things, conditions emission signals  192  and excitation signals  194  to provide bidirectional edge and feature clarification. In the illustrated implementations, this function is accomplished using an excitation signal filter having appropriate smoothing characteristics and symmetrical rise and fall characteristics, and a matched emission signal filter. In some implementations, such as shown in  FIG. 4 , module  310  also includes a hardware-implemented normalization factor generator  450 . Generator  450  generates a normalization factor  452  that is provided to compensation processor  460 . Based on normalization factor  452 , processor  460  adjusts emission signals  192  for noise in excitation signals  194 . The resulting normalized emission signal  312  is shown in  FIG. 3  in dotted lines to emphasize that it is the product of an optional configuration. In some other embodiments, a software application executed on computer  350 , together with a digital signal processor board in the computer, implement the functions of generating a compensating factor and adjusting emission signals  192  to compensate for noise in excitation signals  194 . The result is normalized emission signal data  374  stored in system memory  370  of computer  350  for further processing and/or display. The functions of certain components of scanner  300  and computer  350  are interchangeable in some implementations. As a non-limiting example, some or all of the functions of digital signal processor board  380 , as well as those of scanner control and analysis applications executables  372  may, in some implementations, be carried out by noise compensation module  310 . The functions of module  310  are now further described, first in an example in which module  310  carries out both bi-directional edge clarification and noise compensation, and then in an example in which the latter function is carried out by software executing on computer  350 . 
       FIG. 4  is a functional block diagram of one implementation of noise compensation module  310 , referred to as module  310 A. Using primarily hardware components, illustrative module  310 A adjusts emission signal  192  to compensate for noise in excitation source  120 , thereby providing normalized emission signal  312 . Module  310 A includes a series of a number N gain generators  410 . Under the control of computer  350 , gain generators  410  provide adjustable gains so that excitation signal  194  is normalized irrespective of excitation source. This normalization is provided to compensate for differences in the amplitude of excitation signal  194  due to differences in optical parameters of scanner optics and detectors  100  at different wavelengths of excitation beam  135 . These optical parameters include the percentage of light of different wavelengths that passes through dichroic mirror  136 , optical losses due to mirror reflection that may vary according to wavelength, the response characteristics of excitation detector  110  as a function of wavelength, and other factors that will be appreciated by those of ordinary skill in the relevant art. 
     Gain generators  410  may be implemented in accordance with any of a variety of conventional techniques, or ones that may be developed in the future, for changing the amplitude of a signal. The gains provided by each of generators  410  may be predetermined based on calibration protocols; for example, variable resistors may be adjusted by a technician during manufacture so that a standard amount of power provided by each of excitation sources  120  results in a same voltage for gain-normalized excitation signal  422 . Alternatively, this adjustment function could be performed automatically by scanner control and analysis executables  372 . For example, under the control of executables  372 , each of excitation sources  120  may successively be enabled and a representative value of excitation signal  194  be calculated for each. In accordance with known techniques, these calculated values may be provided to generators  410  to change gain parameters to achieve signal normalization. 
     Module  310 A also includes multiplexer  420  that, under the control of computer  350  in this implementation, selects the normalized excitation signal provided by the gain generator corresponding to the one of excitation sources  120  that is operational. For example, during a period when computer  350  has made excitation source  120 A operational, and assuming for illustrative purposes that gain generator  410 A has been calibrated to source  120 A, then computer  350  provides an appropriate enabling or control signal to multiplexer  420  so that the signal from generator  410 A is selected. Multiplexer  420  may select from any number of “N” inputs to provide, in the illustrated implementation, one selected output, shown in  FIG. 4  as gain-normalized excitation signal  422 . Any of numerous conventional or future multiplexers or switches may be used to provide this function. 
     Another component of module  310 A in the illustrated implementation is gain generator  490 . Generator  490  adjusts the gain of emission signal  192  in accordance with known techniques to provide that the input to filter  440  is within a nominal range of amplitudes or, alternatively, has a nominal steady-state component. Thus, for example, if the emissions of a particular fluorophore in a particular assay occur over a relatively small dynamic range, the emission signal from that fluorophore may optionally be adjusted by gain generator  490  to provide a proportionately larger-range signal for filtering and subsequent sampling. The magnitude of the gain adjustment may, in some implementations, be user selected. For example, a user may employ a graphical user interface (not shown) or other input technique to specify to scanner control and analysis executables  372  what the gain provided by gain generator  490  should be. This determination typically is made based on the fluorophores used in a particular assay and a list of illustrative gains that may be presented to the user in a pull down menu of the graphical user interface or in accordance with any of a variety of other known techniques. In other implementations, the gain value may be determined automatically by scanner control and analysis executables  372 . For example, executables  372  may measure emission signal  192  to determine its low-frequency components, peak-to-peak amplitudes, or other indicators of dynamic range. In accordance with known techniques, executables  372  may then consult a look-up table included, for example, in calibration data  376 , to compare the measured indicators with nominal values, and adjusts the gain accordingly. 
     Also included in noise compensation module  310 A is emission filter  440 . Emission filter  440  performs an anti-aliasing function so that normalized emission signal  312  may be digitized without aliasing errors. In the illustrated implementation, filter  440  is a low-pass filter. As noted, it is not uncommon for high-frequency noise to be present in the outputs of less expensive lasers, and the magnitude of this noise may constitute a substantial portion (e.g., 60%) of the magnitude of the signal. Generally, emissions of fluorophores are linearly related to their excitation throughout a range of interest in typical scanner applications. Therefore, high frequency noise from the lasers in excitation beam  135  produces high frequency noise of the same character in emission signal  192  and adjusted emission signal  462  and, of course, in excitation signal  194 . 
     The low-pass, anti-aliasing characteristics of filter  440  are designed, in accordance with known techniques, based on a rate at which normalized emission signal  312  will be digitally sampled. This sampling rate, in turn, is based on a desired scan rate and a desired resolution of the scanned image. These considerations are now described in relation to  FIGS. 5A and 5B . 
       FIG. 5A  is a simplified graphical representation of a probe feature for detection and processing by scanner  300 . Generally, the term “probe feature” is used in this context to refer to a region of a probe array made up one or more probes that are designed to detect a same target or portion of a target, or to provide a control to verify the detection of that target or portion of a target. In a spotted probe array, a probe feature may be a single spot of a biological material intended to contain one species of polymer. In a synthesized probe array, a probe feature may include many thousands of oligonucleotides designed for a perfect match with a same target sequence, or a probe feature may include thousands of nucleotides designed for a mismatch (for control purposes) with a same target sequence. 
       FIG. 5A  shows idealized probe feature  500  in the form of a single circular spot that may be deposited, for example, by an Affymetrix® 417™ or 427™ Arrayer. It will be understood that a probe feature may be any shape, including irregular shapes. Spot  500  may be, as an illustrative example, one of features  230  of the spotted probe array of  FIGS. 2A and 2B . In the manner described above, objective lens  145  scans over probe feature  500  (and, typically, other probe features of the probe array) in bi-directional arcs. An illustrative scan  520  is shown in  FIG. 5A . It will be understood that  FIG. 5A  is not necessarily drawn to scale, and that the ratio of the radius of the arc of scan  520  to the radius of feature  500  is illustrative only. 
     Also, probe feature  500  moves under objective lens  145 , as represented by direction  244  of  FIGS. 2B and 5A  that, as noted, may be referred to for convenience as the “y” direction. Thus, in the illustrated implementation, arm  200  scans in an arc in one direction, shown as left-to-right scan  520  in  FIG. 5A . Translation stage  242  is then moved incrementally by a stepping motor (not shown) in y-direction  244  and arm  200  then scans back in the opposite direction, shown as right-to-left arcuate scan  522 . Translation stage  242  is again moved in direction  244 , and so on in scan-step-scan-step sequences. In this example, the terms “scan” or “scan line” thus will be understood to apply to a scan of a line or an arc, typically each “scan” referring to the movement along the line or arc in one direction. However, a scan may also be repeated in one direction, or bi-directionally, multiple times, and the terms “scan” or “scan line” may refer to these repeated scans in some contexts. Returning to the present specific example in which scans  520  and  522  are referred to as separate scans, the distance between these scans thus corresponds to the distance that translation stage  242  is moved in each increment, although it will be understood that the distance shown in  FIG. 5A  is not necessarily to scale and is illustrative only. It will be understood that any other combination of scanning and stepping is possible in alternative implementations, and that scanning and moving of translation stage  242  may occur at the same or at overlapping times in some implementations. Translation stage  242  need not be stepped in some implementations, but may, for example, be moved continuously. 
       FIG. 5B  is a plot having a pixel clock axis  530  showing when clock pulses  532  occur. Axis  530  in the illustrated implementation is a spatial axis; that is, each of clock pulses  532  occurs in reference to the radial location of arm  200  during each scan, as described in greater detail below. Thus, with reference to the position of translation stage  242  indicated by scan  520 , a clock pulse  532 A occurs prior to arm  200  passing over feature  500  from the left as shown in  FIGS. 5A and 5B . (For sake of clarity of illustration only, vertical dotted lines are provided between  FIGS. 5A and 5B  to illustrate this alignment.) As another example, clock pulse  532 C occurs with respect to scan  520  when arm  200  has just passed over portions of feature  500  indicated by pixel areas A and K. These areas are referred to as pixel areas because a digital value is assigned to each such area in the illustrated implementation based on the strength of a filtered emission signal associated with that area. In accordance with known techniques, clock pulses  532  enable the digital sampling of the filtered emission signal. 
     As will be appreciated by those of ordinary skill in the relevant art, the Nyquist criterion may be applied to determine the appropriate low-pass characteristics of filter  430  based on a desired sampling rate. As noted, clock pulses  532  are spatially rather than temporally determined in the illustrated implementation. Moreover, in some aspects of the illustrated implementation, galvanometer  216  is driven by a control signal provided by computer  350  such that the velocity of arm  200  in x-direction  243  is constant in time during those times when arm  200  is over probe feature  500  (and, typically, over other features of the probe array being scanned). That is, dx/dt is a constant (and thus the angular velocity varies) over the probe-scanning portions of each arc and, in particular, it is a constant during the times when clock pulses are generated to enable digital sampling. As is evident, dx/dt must be reduced to zero between each successive scan, but this deceleration and reversal of direction takes place after arm  200  has passed over the probe feature (or, more generally, the probe array). The design and implementation of a galvanometer control signal to provide constant dx/dt are readily accomplished by those of ordinary skill in the relevant art. 
     Thus, the approximate sampling rate may readily be calculated based on the desired scanning speed (dx/dt) and desired pixel resolution. To provide an illustrative example, a spot deposited by an Affymetrix® 417™ Arrayer typically has a diameter of approximately 200 microns. Spotted probe arrays made using this instrument typically may be deposited over a surface having a width of about 22 millimeters on a microscope slide that is 25 millimeters wide. In order to achieve pixel resolution of about 10 microns, a sampling rate of about 160 kHz is sufficient for scanning speeds typical for scanners used with respect to these probe arrays, such as the Affymetrix® 428™ scanner. Other sampling rates, readily determined by those of ordinary skill, may be used in other applications in which, for example, different scanning speeds are used and/or different pixel resolutions are desired. The desired pixel resolution typically is a function of the size of the probe features, the possibility of variation in detected fluorescence within a probe feature, and other factors. The desired scanning speed typically is a function of the size of the probe array to be scanned, the amount of a time that a user may wish to wait for the scanning to be completed, the response characteristics of the fluorophores, the response characteristics of emission detector  115 , the response and operational characteristics of galvanometer  216 , and a variety of other factors. 
     In order to avoid aliasing errors, filter  440  should have a low-pass cutoff frequency of one half or less of the sampling frequency, as those of ordinary skill will appreciate based on the Nyquist criterion. Thus, for example, filter  440  as implemented in the Affymetrix® 428™ scanner is designed in accordance with known techniques to have a cut-off frequency of 33 kHz in some implementations and 67 kHz in other implementations. As will be evident to those of ordinary skill in the relevant art, the lower cut-off frequency achieves somewhat greater smoothing at the expense of a potential loss in signal accuracy. In implementations in which the command signal driving galvanometer  216  is not designed to provide constant dx/dt but rather, for example, a constant angular velocity over the probe-scanning area, the appropriate cut-off frequency dictated by the Nyquist criterion should take into account variation in the sampling rate for different portions of the arc assuming that it is desired to provide clock pulses that are constant in the x direction. 
     Noise compensation module  310 A also includes excitation signal filter  430  that has the same design characteristics as, i.e., it is matched with, emission signal filter  440 . The reason for matching filters  430  and  440  with each other is to provide that the delay through both filters is the same. If the delays were different, then filtered excitation signal  432  and filtered emission signal  442  would no longer be spatially correlated. That is, a value of filtered excitation signal  432  at a particular time “t” would represent the excitation of a particular fluorophore at a position “p,” but the value of filtered emission signal  442  at the same time “t” would represent the emission of a fluorophore that was excited at a position either before or after position “p” in the scanning arc. 
     Loss of spatial correlation could interfere with techniques described herein to normalize emission signals to compensate for noise in laser excitation signals. As described below, normalized emission signal  312  is determined in this implementation by adjusting filtered emission signal  442  by a normalization factor  452 . Factor  452  is determined by comparing a nominal excitation value with filtered excitation signal  432 . The nominal excitation value can be derived in a variety of ways, such as by low-pass filtering or by taking an average or other statistical measure of large numbers of samples over a relatively long period so that the impact of noise components is minimized. Also, a nominal value can be predetermined by manual calibration or other techniques, and the value stored in calibration data  376  for reference. In essence, emission signals are adjusted to compensate for variations in the excitation signals that gave rise to them. If spatial correlation is not maintained, then this cause and effect relationship may be lost and erroneous adjustments may result. However, approaches other than matched filters may be taken to provide spatial correlation. For example, in alternative embodiments, any mismatches in the delays of filters  430  and  440  may be compensated for either in hardware (e.g., by introducing a compensating delay with respect to one or the other signal in accordance with known techniques) or in software (e.g., by realigning sampled emission and excitation signals to offset delays). 
       FIGS. 5A–5D  further illustrate these points. In these figures, it is illustratively assumed that executables  372  initiates clock pulse  532 D at a time “t.” This clock event is determined by the receipt of a signal from transducer  215  indicating that excitation beam  135  is located over a radial position in the scanning arc shown with reference to scan  520  as radial position  525 C′. (Transducer  215  provides a signal with the same value when beam  135  is located over the same radial position for scan  522 , which is labeled as radial position  525 C″.) Executables  372  retrieves from galvo position data table  378  a value of the signal from transducer  215  that corresponds to radial positions  525 C′ and  525 C″. This value also corresponds to a position on each of every other scan that intersects with constant radial position line  525 C of  FIG. 5A , which is parallel to direction  244  of translation stage  242 .) This retrieved value is compared to the signal from transducer  215  until it is determined that the values are equal, causing executables  372  to initiate clock pulse  532 D. In the illustrated implementation, the radial position values in galvo position data table  378  are predetermined so that each of constant radial position lines  525  (e.g.,  525 A,  525 B, through  525 K of the example of  FIG. 5A ) are positioned at an equal distance perpendicular to direction  244 . This feature facilitates the software translation of pixels from polar coordinates to Cartesian coordinates. 
     Thus, returning to the example of clock pulse  532 D initiated at time “t,” it is illustratively assumed that filtered excitation signal  432  has a value at that time that is shown in  FIG. 5D  as filtered excitation voltage  580 D. Voltage  580 D therefore may be spatially correlated with radial position  525 C′ (and with the position at time “t” of translation stage  242 ). However, because voltage  580 D has been filtered and thus phase delayed, it typically corresponds with values of gain-normalized excitation signal  422  that occurred earlier in time and therefore at a location on scan  520  to the left of radial position  525 C′. To take into account this spatial translation, it is provided that adjusted emission signal  462  is phase delayed by the same amount. As noted, this result is accomplished by providing that the phase delay characteristics of filters  440  and  430  are matched. For example, the same electrical components may be used, particularly if gain generator  490  provides that adjusted emission signal  462  has approximately the same dynamic range as gain-normalized excitation signal  422 . Thus, because the phase delays for both excitation and emission signals are the same, the value of filtered emission signal  442  sampled as the result of the initiation of clock pulse  532 D, shown as illustrative voltage  550 D in  FIG. 5C , corresponds spatially with excitation voltage  580 D. Alternatively stated, the matched filters provide that a fluorophore located at a position on probe feature  500  represented by position  525 C′, which was excited by voltage  580 D, emitted a signal represented by voltage  550 D, wherein both voltages were sampled at a same time. 
     A further desirable characteristic to be considered in the design of filters  430  and  440  is to provide constant group delay of the filters&#39; input signals irrespective of the frequency components of those inputs. That is, it generally is desirable that the phase delay introduced by filters  430  and  440  be a determinable constant based on the filters&#39; design rather than the characteristics of the input signal. Alternatively stated, it generally is desirable for bi-directional scanning that the rise and fall response characteristics of each of the filters be symmetrical. In the illustrated implementation, these characteristics are accomplished by providing that both of filters  430  and  440  are linear-phase filters, such as Bessel filters. In particular, filters  430  and  440  are high-order Bessel filters, such as 6 th  order or higher, and preferably 11 th  order or higher, Bessel filters. The advantage of providing the feature of symmetrical, matched filters may be illustrated with respect to the example of  FIGS. 6A–6E . 
       FIG. 6A  shows a simplified input waveform  600  such as may be provided as input to filter  440 , i.e., adjusted emission signal  462 . Input waveform  600  has simulated high-frequency noise components that are included within repeating dual pulses  610 A through  610 G (generally and collectively referred to hereafter for convenience as noise pulses  610 ). It will be understood, however, that noise components of signal  462  (and of signal  422 ) typically are not regular and are more complex in frequency and amplitude. 
     Output waveform  615  of  FIG. 6B  is a graphical representation of the output of filter  440  in response to input waveform  600 , assuming that filter  440  is not a linear-phase filter. For example, filter  440  may be a Butterworth filter in this example. A peak  612 A is observable on waveform  442 A having a rising edge  616 A that is steeper and of a different shape than its falling edge  614 A; i.e., the rising and falling edges are not symmetrical. As is evident, the same asymmetry occurs in response to each of input pulses  610 , as indicated by output pulses  612 A through  612 H. 
     It is now illustratively assumed that output waveform  615  is the result of scan  520  in the left-to-right direction, and that a successive scan  522  in the opposite direction is made over a probe feature that has a constant concentration of fluorophores between and including the two scans. Equivalently, it may be assumed that the stepping motor does not advance translation stage  242  between the scans. To obtain the same result irrespective of the direction of the scan, output waveform  615  should have the same shape irrespective of which direction the scan was taken (although the waveforms will be displaced in time by a factor of twice the phase delay of the filter). However, as can be seen from  FIG. 6B , this desired symmetry will not occur since the rising and falling edges of pulses  612  are asymmetrical. Improved smoothing and perhaps greater symmetry can be accomplished by higher-order filters that do not have the characteristic of constant group delay, as shown by  FIG. 6C . Output waveform  620  of  FIG. 6C  is the response of such a filter to input waveform  600 . Pulses  622  of  FIG. 6C  are smoother and somewhat more symmetrical than pulses  612  of  FIG. 6B , but the problem of directional-dependent inconsistency remains. 
     In contrast, output waveform  630  of  FIG. 6D  is the simulated response of filter  440  implemented as a Bessel filter, and it may be observed that the resulting pulses are substantially symmetrical. For example, rising edge  636 A is substantially the mirror image of falling edge  634 H. The degree of symmetry generally may be improved by implementing filter  440  (and providing matched filter  430 ) as higher-order Bessel filters, as shown by output waveform  640  of  FIG. 6E . 
     The advantages of using symmetrical filters for bi-directional scanning may further be appreciated with reference to  FIGS. 7A–7C  and  8 A– 8 C.  FIG. 7A  is a graphical representation of an input waveform  700  that is illustratively assumed to be provided to asymmetrical emission signal filter  440 . Waveform  800  of  FIG. 8A  is the same as waveform  700 , except that it is illustratively assumed to be provided to filter  440  implemented as a symmetrical filter, such as Bessel filters. Both waveforms  700  and  800  are idealized for clarity of illustration in that no noise is present and the pulses are shown as simple step functions. 
       FIG. 7B  shows output waveform  739  resulting from a scan  720  in a first direction, and  FIG. 7C  shows output waveform  749  resulting from a scan  522  in an opposite direction, both in the context of an implementation of filter  440  (and thus filter  430  to provide matching) as asymmetrical filters. Similarly,  FIG. 8B  shows output waveform  839  resulting from a scan  820  in a first direction, and  FIG. 8C  shows output waveform  849  resulting from a scan  522  in an opposite direction, both in the context of an implementation of filters  430  and  440  as symmetrical filters. The voltage waveforms of  FIGS. 7A–7C  and  8 A– 8 C are shown as functions of consecutive clock pulses  732  and  832 , respectively, on spatial pixel clock axes. With reference to  FIG. 7B , output waveform  739  results from scanning in left-to-right scan direction  720  in relation to spatial pixel clock axis  730 . That is, input waveform  700  results from scanning at positions to the left of the radial position represented by pixel clock position  732 D and proceeding toward the radial position represented by pixel clock position  732 K. As seen from output waveform  739 , the portion of the rising edge of that waveform between positions  732 D and  732 E is of a different shape than the portion of the falling edge between positions  732 F and  732 G. This difference is graphically represented by pixels  735  aligned below corresponding pixel clock positions. For example, if waveform  739  were sampled by a pixel clock pulse corresponding to position  732 D, the sampled value would be relatively small. For convenience, a small value (e.g., relatively low intensity of filtered emission signal  442 ) is shown as a dark pixel, such as pixel  735 A. If waveform  739  were sampled at position  732 E, at the top of the rising edge, the sampled value would be relatively large, as represented by white pixel  735 B indicating a high intensity emission signal. A sample taken at position  732 F along the falling edge provides a middle value, as represented by pixel  735 C in cross hatching. The area scanned in direction  720  between positions  732 D and  732 K would be represented by the following sequence of pixel intensities as indicated by pixels  735 : dark—white—mid—dark—dark—white—mid—dark. Each level of intensity is indicative of a different degree of emission by fluorophores at locations corresponding to the pixel clock positions (although, as noted, a phase delay is anticipated). In  FIG. 7C  it is illustratively assumed that the same input waveform  700  is provided to the same filter, except that the scan is in direction  722 , i.e., starting from position  732 K and moving toward position  732 D. Because of the asymmetry of the rising and falling edges after filtering, the samples taken in this reverse positional order result in a different sequence of pixel intensities, as indicated by pixels  745 : dark—mid—white—dark—dark—mid—white—dark. 
     Two observations can thus be made by comparing these two sequences. One observation is that the two pulses of input waveform  700  are measured differently based on the direction of scanning: in the 720 direction the pulses are measured as white—mid, whereas in the 722 direction the same pulses are measured as mid—white. That is, in successive bid-directional scans, spatial transitions in input values provide inconsistent sampling results. The second observation is that the measured pulses are shifted spatially by twice the phase delay of the filter. This phase delay need not, and generally will not, be an integer number of pixel positions, but is a real number representing a spatial shift determined by the phase delay characteristics of the filter. 
     The results of these effects can be seen in  FIG. 7D , which is a simplified graphical representation of pixels resulting from successive bidirectional scans of a probe feature in which adjusted emission signal  462  is represented by input waveform  700  for all scans in both directions. The pixels are aligned spatially along pixel clock axis  730 , as in  FIGS. 7B and 7C . In order to accommodate the phase delay introduced by emission filter  440 , the spatial width of the scan in either direction (a distance D equal to the distance between ten clock pulses in this example) is greater than the spatial width of the probe feature being scanned (eight clock pulses); i.e., the feature can be said to have been “over-scanned” in both directions. Although the phase delay in this example is shown as equal to the distance between successive clock pulses, this is only an illustrative example. As noted, the delay in general is measured as a real number that may be expressed as fractions (any real number) of distances between clock pulses, i.e., fractional pixels. 
       FIG. 7E  is a graphical representation of the pixels of  FIG. 7D  shifted so as to graphically compensate for the effects of phase delay. The pixels at the beginning and end of each scan have been eliminated from this representation so that the external edges of the feature representation can be more clearly seen. This shifted representation may, for example, be presented to users in a graphical user interface, or the data associating the pixels in this manner may be stored in computer  350  for further image and/or signal processing. These tasks may be accomplished in accordance with any of a variety of conventional techniques well known to those of ordinary skill in the art whether implemented in hardware, software, or a combination thereof. As indicated by  FIG. 7E , transient pixel intensities appear indistinct. In particular, the left hand edge of the feature as represented by input waveform  700 , as detected at the output of asymmetric filter  440  of this example, has a zipper-like pattern of alternating high and mid-intensities shown by vertically alternating pixels  735 B and  745 B. The right hand edge has the same distorted quality, as shown by vertically alternating pixels  735 G and  745 G. The same distortion is present at transient points within the feature, as indicated by vertically alternating pixels  735 C and  745 C, and by vertically alternating pixels  735 F and  745 F. 
       FIGS. 8D and 8E  present the same information as described above with regard to  FIGS. 7D and 7E , respectively, except that  FIGS. 8D and 8E  are based on the assumption of  FIGS. 8B and 8C  that filter  440  is a symmetrical filter. As is indicated by  FIGS. 8D and 8E , a phase delay is also introduced by the symmetric filter. However, transients in the intensity of filtered emission signal  442  are not distorted. Rather, as indicated by the vertical alignment of consistently high-intensity pixels, the zipper effect is avoided and the transient points are clear. 
     Returning now to  FIG. 4 , two additional components of noise compensation module  310 A remain to be described. Normalization factor generator  450  compares filtered excitation signal  432  to excitation reference  476 . The purpose is to provide a normalization factor  452  that provides a measure of a deviation of filtered excitation signal  432  from a nominal value. This deviation typically is due to noise in excitation beam  135  generated by excitation source  120  (e.g., the laser operational at the period of interest) that thus appears in excitation signal  194  and gain-normalized excitation signal  422  and, in filtered form, in filtered excitation signal  432 . The deviation may also be due, in some implementations, to long-term drift in excitation beam  135 . For example, lasers may degrade over periods of weeks, months, or years so that the magnitude of their steady state output declines. This long-term drift, which may be positive or negative, may be compensated for by adjusting the gain of the appropriate one of gain generators  410 B. Alternatively, the excitation reference component of calibration data  376  may be adjusted accordingly. In either case, if the long-term drift reaches a threshold level, a user may be advised that excitation source  120  has degraded and should be repaired or replaced. The threshold level may, for example, be a predetermined percentage of a nominal laser output value supplied by the laser manufacturer and stored as a component of calibration data  376 . The notification to the user may be accomplished for example by an appropriate graphical user interface of computer  350 , all in accordance with conventional techniques well known to those of ordinary skill in the relevant art. 
     With respect to the objective of compensating for laser noise, excitation reference  476  typically, but not necessarily, represents a nominal expected value of filtered excitation signal  432  over a time period substantially greater than that of the lowest expected noise frequency, but shorter than the time over which significant laser drift typically occurs. This period is selected such that an average or other statistical measure of signal  432  may reliably be determined. For example, monitored filtered excitation signal  434 , equal to or representative of filtered excitation signal  432 , may be provided to computer  350  for digital sampling over a period of one or more scans. In accordance with known techniques, the sampled signal may be statistically processed to provide, for example, an average or nominal value of signal  432  for that scan that may be used as excitation reference  476  for the next scan. Alternatively, each scan may be done twice: once to determine an average value and once to determine actual values including noise. Thus, the value of excitation reference  476  may be updated as frequently as every scan or less. Alternatively, reference  476  may be predetermined based on an initial calibration of excitation source  120 , or based on manufacturer&#39;s specifications, and stored as a component of calibration data  376 . In yet another alternative implementation, low-pass filter  431  may be used to remove all expected noise components from filtered excitation signal  432 , and this low-frequency signal, shown as  476 ′, may be used as an excitation reference. This implementation is represented in dashed lines in  FIG. 4  to indicate its optional application. 
     As will now be appreciated by those of ordinary skill in the art, many other techniques are possible in hardware, software, or both, for providing an excitation reference that represents filtered excitation signal  432  with noise components substantially removed. In many cases, moreover, it is desirable to provide that, at a standard value of gain generator  490 , each implementation of each excitation source  120  of each scanner  300  provides a standard value of filtered emission signal  442  when exciting a standard fluorophore sample. In some implementations, therefore, a known concentration of fluorophores is prepared as a calibration slide to be scanned by each of a series of manufactured scanners  300 . Gain generator  490  is set at a nominal, standard, value, preferably one determined with respect to the dynamic range of the fluorophore. A photomultiplier tube or other detector is set to measure filtered emission signal  442 . In some implementations, adjusted emission signal  462  may be measured instead. The power of excitation beam  135  is also measured by, for example, measuring filtered excitation signal  432  (with the corresponding gain generator  410  set to a standard value) in accordance with any of a variety of conventional measuring techniques. For each of excitation sources  120 , e.g., for each of lasers  120 A and  120 B of the illustrated implementation, the excitation source is adjusted to increase or decrease excitation beam  135  until the measured value of filtered emission signal  442  (or of signal  462 ) is a standard value. The value of filtered excitation signal  432  at this calibration setting is stored in calibration data  376  and thenceforth serves as excitation reference  476  for that excitation source  120  for that scanner  130 , or as a basis for determining an appropriate excitation reference. In alternative implementations, instead of adjusting the excitation source to increase or decrease beam  135 , the adjustment may be made to gain generator  490 , and/or to the gain of emission detector  115 . In either case, excitation reference  476  is a constant value, and is not determined by, for example, averaging scans or low-pass filtering as described above. Rather, reference  476  is a calibrated value unique to the instrument and, generally, constant for the life of the instrument or a period of time over which consistent experimental results are desired. A significant advantage of the calibration approach leading to a constant excitation reference  476  for each scanner  130  instrument is that, even if excitation source  120  degrades over time, a user will be able to replicate experiments and obtain the same measurements over time. 
     In one implementation, normalization factor generator  450  may be an analog multiplier/divider device, such as is available from a variety of commercial suppliers including Analog Devices, Inc. of Norwood, Mass., or one of numerous other analog and/or digital devices that perform multiplication, division, and/or comparative functions. In the illustrated implementation, generator  450  multiplies or divides filtered excitation signal  432  and excitation reference  476  (or  476 ′) to provide a ratio between the two. For example, if reference  476  has a value of 1.00 and the value of signal  432  is 1.25, then the value of normalization factor  452  at that time (hereafter, for convenience, the “instantaneous” value) is 1.00/1.25=0.80. That is, in this illustrative implementation, the comparison between a steady state measure of signal  432  and the instantaneous value of signal  432  is provided by dividing an average value of signal  430  by the instantaneous value of signal  430 . Any of various other statistical comparisons may be used in alternative implementations, as will now be appreciated by those of ordinary skill in the relevant art. 
     Comparison processor  460  applies normalization factor  452  to filtered emission signal  442 . Comparison processor  460  may also any of numerous analog multiplier/divider device or other devices such as noted above with respect to generator  450 . In the illustrated implementation, processor  460  multiplies the instantaneous value of filtered emission signal  442  by normalization factor  452  to provide normalized emission signal  312 . Thus, in the illustrated implementation, generator  450  and processor  460  together implement a function that may be represented as:
 
signal 312( t )=signal 442( t )*(average signal 432/signal 432( t ))
 
where (t) indicates instantaneous values over time.
 
     Signal  312  may in some implementations be provided to computer  350  for sampling as enabled by pixel clock pulses generated by computer  350 , as described above. In other implementations, the generation of pixel clock pulses and their application to signal  312  may be done by an appropriate device located in scanner  300 . For example, as shown in  FIG. 3 , pixel clock  305  may be implemented in scanner  300  by a complex programmable logic device (CPLD) such as is commercially available from Altera Corporation of San Jose, Calif., and other suppliers. 
       FIG. 9  is a functional block diagram showing an alternative implementation in hardware and software of the functions just described with respect to the primarily hardware implementation of  FIG. 4 . In particular, the functions of elements  910 ,  920 ,  930 ,  940 , and  960  of  FIG. 9  are similar to those described above with respect to elements  410 ,  420 ,  430 ,  440 , and  460  of  FIG. 4 , respectively. However, in the implementation of  FIG. 9 , the functions described above with respect to normalization factor generator  450  and comparison processor  460  are performed by computer  350 . The result in the implementation of  FIG. 9  is normalized emission signal data  374  that provide information similar to that contained in normalized emission signal  312  as shown in  FIG. 4 . 
     It will be understood that the embodiment of computer  350  shown in  FIGS. 3 ,  4  and  9  is exemplary only, and that many alternative implementations are possible. For example, the functions of computer  350  may be performed by one or more components of scanner  300  rather than being performed by an external computer. For instance, scanner  300  may include a microprocessor with associated firmware for performing some or all of the functions ascribed herein to computer  350 . 
     In the illustrated embodiment, computer  350  may be located locally to scanner  300 , or it may be coupled to scanner  300  over a local-area, wide-area, or other network, including an intranet and/or the Internet. Computer  350  may be a personal computer, a workstation, a server, or any other type of computing platform now available or that may be developed in the future. As shown in  FIG. 4 , computer  350  includes a process controller  462  for performing control and analysis functions with respect to scanner  300  as described below. Typically, computer  350  also includes known components such as CPU  355 , operating system  360 , system memory  370 , memory storage devices  380 , and input-output controllers  375 , all of which typically communicate in accordance with known techniques such as via system bus  390 . In the illustrated implementation, computer  350  also includes digital signal processor board  380 , which may be any of a variety of PC-based DSP controller boards, such as the M44 DSP Board made by Innovative Integration of Simi Valley, Calif. A variety of other components may be included in computer  350 , as is well known by those of ordinary skill in the relevant art. 
     In reference to  FIG. 9 , filtered excitation signal  932 , corresponding to filtered excitation signal  432  described above, is provided to line driver  931  that, in accordance with known techniques, provides signal  932 ′ to DSP board  380  of computer  350 . Similarly, filtered emission signal  942 , corresponding to filtered emission signal  442  described above, is provided to line driver  941  that provides signal  942 ′ to DSP board  380 . In accordance with known analog-to-digital sampling techniques, board  380  samples signals  932 ′ and  942 ′ based on pixel clock sampling pulses. These pulses may be provided by pixel clock CLPD  305 , or they may be generated by aspects of executables  372  by comparing radial position information from galvo position transducer  215  with data in galvo position data table  378 . In the former implementations, CLPD  305  performs the functions of computer  350 , and may also store data such as that in table  378 . Optionally, prior to sampling, board  380  may include anti-aliasing filters (such as filters  1030  and  1040  of  FIG. 10 ) designed in accordance with the Nyquist criterion as noted above to further ensure that aliasing errors do not occur when signals  932 ′ and  942 ′ are sampled. 
     In this alternative implementation software-implemented functional elements of executables  372  perform the functions described in reference to  FIG. 4  with respect to the operations of normalization factor generator  450  and comparison processor  460 . That is, executables  372 , in cooperation with other elements of computer  350  such as CPU  355  and operating system  380 , generates a compensation factor that is based on a comparison between a reference excitation value and, in some implementations, each sampled excitation value. Executables  372  then applies this factor to each corresponding sampled emission signal to provide normalized emission signal data corresponding to each sample of the emission signal. Thus, the functional elements of executables  372  comprise sets of software instructions that cause the described functions to be performed. These software instructions may be programmed in any programming language, such as C++ or another high-level programming language. Executables  372  may therefore be referred to as “a set of scanner control and analyzing instructions,” and its functional elements may similarly be described, for example, as sets of normalization factor generating instructions (as represented by generator  1050 ) and comparison processing instructions (as represented by processor  1060 ). 
     These operations are shown in greater detail in  FIG. 10 , which is a functional block diagram of aspects of computer  350  that generate normalization factors for each sampled excitation signal and applies those factors to filtered emission signals to obtain normalized emission signal data. In accordance with any of a variety of known techniques, analog to digital converter  1035  digitizes samples of signals  932 ′ to generate excitation samples  1037 , which are provided by to normalization factor generator  1050  of executables  372 . Similarly, analog to digital converter  1045  digitizes samples of signals  942 ′ to generate emission samples  1047 , which are provided by to comparison processor  1060  of executables  372 . For ease of reference, a pair of samples  1037  and  1047  sampled according to the same sampling pulse will be referred to as a particular instance of those samples. 
     Excitation reference  1076  of calibration data  376  also is provided to generator  1050 . Reference  1076  is a reference excitation value derived in accordance with any of the techniques described above with respect to excitation reference  476 . 
     Generator  1050  performs functions similar to those described above with respect to generator  450 . For example, in some implementations, generator  1050  determines an instance of compensation factor  1052  by dividing reference  1076  by the value of excitation sample  1037  for that instance. This instance of factor  1052  is multiplied by the corresponding instance of emission sample  1047  to obtain the corresponding instance of normalized emission signal data  374 . Thus, in the illustrated and non-limiting implementation, each instance (I) of data  374  is derived in accordance with the algorithm:
 
data 374( I )=sample 1047( I )*(reference 1076/sample 1037( I ))
 
     Typically, generator  1060  and processor  1070  are implemented as software instructions in any appropriate programming language, such as C++, and compiled for inclusion in executables  372  that are executed on computer  350  of the illustrated implementation. In particular, system memory  370  of computer  350  may be any of a variety of known or future memory storage devices. Examples include any commonly available random access memory (RAM), magnetic medium such as a resident hard disk or tape, an optical medium such as a read and write compact disc, or other memory storage device. Memory storage devices  380  may be any of a variety of known or future devices, including a compact disk drive, a tape drive, a removable or internal hard disk drive, or a diskette drive. Such types of memory storage devices  380  typically read from, and/or write to, a program storage medium (not shown) such as, respectively, a compact disk, magnetic tape, removable or internal hard disk, or floppy diskette. Any of these program storage media, or others now in use or that may later be developed, may be considered a computer program product. As will be appreciated, these program storage media typically store a computer software program and/or data. Computer software programs, also called computer control logic, typically are stored in system memory  370  and/or the program storage medium used in conjunction with memory storage devices  380 . 
     In some implementations, a computer program product is described comprising a computer usable medium having control logic (computer software program, including program code) stored therein. The control logic, when executed by processor  355 , causes processor  355  to perform the functions of scanner control and analysis executables  372 , including generator  1050  and processor  1060 . In other embodiments, these and other functions of executables  372  may be implemented primarily in hardware using, for example, a hardware state machine. Implementation of the hardware state machine so as to perform the functions of executables  372  described herein will be apparent to those skilled in the relevant art. 
     Having described various embodiments and implementations, it should be apparent to those skilled in the relevant art that the foregoing is illustrative only and not limiting, having been presented by way of example only. Many other schemes for distributing functions among the various functional elements of the illustrated embodiment are possible. The functions of any element may be carried out in various ways in alternative embodiments. 
     Also, the functions of several elements may, in alternative embodiments, be carried out by fewer, or a single, element. For example, excitation signal filter  430  and emission signal filter  440  of the implementation shown in  FIG. 4  may, in other implementations, be replaced by a single anti-aliasing filter that operates on the output of comparison processor  460  to provide normalized emission signal  312 . As another example, the functions of gain generators  410  could alternatively be performed by multiplexer  420 , or by computer  350 . 
     Similarly, in some embodiments, any functional element may perform fewer, or different, operations than those described with respect to the illustrated embodiment. Also, functional elements shown as distinct for purposes of illustration may be incorporated within other functional elements in a particular implementation. Furthermore, the sequencing of functions, or portions of functions, generally may be altered. For instance, the functions of gain generator  490  may be performed after those of emission signal filter  440 . 
     Certain functional elements, files, data structures, and so on, are described in the illustrated embodiments as located in system memory  370  of computer  350 . In other embodiments, however, any or all of these may be located on, or distributed across, computer systems or other platforms that are co-located and/or remote from each other. In addition, it will be understood by those skilled in the relevant art that control and data flows between and among functional elements and various data structures may vary in many ways from the control and data flows described above. More particularly, intermediary functional elements may direct control or data flows, and the functions of various elements may be combined, divided, or otherwise rearranged to allow parallel processing or for other reasons. Also, intermediate data structures or files may be used and various described data structures or files may be combined or otherwise arranged. Numerous other embodiments, and modifications thereof, are contemplated as falling within the scope of the present invention as defined by appended claims and equivalents thereto.