# Patent

## Title
Image acquisition, processing, and display

## Abstract

Image data is acquired, processed, and/or displayed in accordance with an embodiment of the present disclosure to display, monitor, and/or demonstrate the progress of an experiment substantially in real-time and with high sensitivity. In one embodiment, at least one time-resolved value of spatially distributed polarization change data is provided and displayed. Advantageously, real-time processing and display of data is provided such that discussion and collaboration about the experiment may occur, time-resolved data is not lost, and resources are not wasted.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation-in-part of U.S. patent application Ser. No. 09/838,700 filed on Apr. 19, 2001 now U.S. Pat. No. 7,023,547, which is a continuation-in-part of U.S. patent application Ser. No. 09/614,503, filed on Jul. 11, 2000, now U.S. Pat. No. 6,594,011, the full disclosures of which are incorporated by reference herein for all purposes.


This application is related to U.S. patent application Ser. No. 10/847,754 filed on May 17, 2004, U.S. patent application Ser. No. 10/847,736 filed on May 17, 2004, U.S. patent application Ser. No. 10/841,988 filed on May 7, 2004, and U.S. patent application Ser. No. 10/046,620 filed on Jan. 12, 2002. The above-mentioned U.S. patent application Ser. Nos. 10/847,754, 10/847,736, 10/841,988, and 10/046,620 are incorporated by reference herein for all purposes.
BACKGROUND
1. Field of Invention
This invention relates to acquisition and processing of data and more particularly to acquisition and processing of microarray data for displaying, monitoring, and/or demonstrating the progress of an experiment substantially in real-time.
2. Discussion of the Related Art
The formation of an array of biologically or chemically active spots on the surface of a substrate for identifying constituents in test material brought into contact with the array is known, such as with a biochip (also referred to as a gene chip, protein chip, microarray, and others). Typically, such processes require spots of, for example, oligonucleotides, cloned DNA, antibodies, peptides, receptors, enzymes, and/or inhibitors, which are processed to exhibit characteristics such as fluorescence, electroluminescence, current change, and/or voltage change, for providing a detectable signature for the presence of constituents in the material being tested.
Typically, microarray experiments have been analyzed at or near the approximate endpoint of reactions, which is presumed to be equilibrium, and real-time and/or time-resolved information have not been provided. Disadvantageously, such endpoint analysis does not allow for monitoring of or collaboration about the process under investigation, thus losing kinetic data, affinity data, and other time-resolved data regarding the process. Such endpoint analysis also does not allow for modification or early termination of the experiment if an error occurs, thus wasting time and resources.
Thus, there is a need for a method and apparatus to gather, process, and display image data which is highly sensitive and substantially at real-time and/or time-resolved.
SUMMARY
Image data is acquired and processed in accordance with an embodiment of the present invention to display, monitor, and/or demonstrate the progress of an experiment substantially in real-time and with high sensitivity. Advantageously, the present invention allows for real-time processing and display of data such that discussion and collaboration about the experiment may occur, time-resolved data is not lost, and resources are not wasted.
In accordance with one embodiment of the present invention, an image processor is provided, including a data acquisition application adapted to receive spatially distributed polarization change data caused by a specimen array; and a data analyzer operably coupled to the data acquisition application, the data analyzer adapted to calculate at least one time-resolved value of the spatially distributed polarization change data.
In accordance with another embodiment of the present invention, an apparatus for imaging is provided, including a light source emitting a polarized light beam; an optical assembly including a light reflection surface, wherein the light beam from the light source is reflected by the light reflection surface to provide an evanescent field adjacent the light reflection surface, the light reflection surface being adapted to allow placing thereon a specimen array such that the specimen array in the evanescent field causes spatially distributed polarization changes in the cross-section of the light beam; and a two-dimensional array detector positioned to detect the spatially distributed polarization changes caused by the specimen array. A processor is operably coupled to the two-dimensional array detector, the processor processing data from the two-dimensional array detector to provide a two-dimensional representation of the spatially distributed polarization changes occurring in the specimen array in real-time.
In accordance with yet another embodiment of the present invention, a method of processing image data is provided, including receiving spatially distributed polarization change data caused by a specimen array; and calculating at least one time-resolved value of the spatially distributed polarization change data.
In accordance with yet another embodiment of the present invention, a method of imaging is provided, including passing a polarized light beam into an optical assembly including a control layer and a light reflection surface to provide an evanescent field with controlled height and intensity adjacent the light reflection surface, a specimen array in the evanescent field causing spatially distributed polarization changes in the cross-section of the light beam; passing the reflected light beam out of the optical structure; and detecting the spatially distributed polarization changes caused by the specimen array. The method further includes processing the detected spatially distributed polarization changes to provide a two-dimensional representation of the spatially distributed polarization changes occurring in the specimen array in real-time.
The scope of the invention is defined by the claims, which are incorporated into this section by reference. A more complete understanding of embodiments of the present invention will be afforded to those skilled in the art, as well as a realization of additional advantages thereof, by a consideration of the following detailed description of one or more embodiments. Reference will be made to the appended sheets of drawings that will first be described briefly.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 is a block diagram of an illustrative system in accordance with an embodiment of the present invention;
FIG. 2 is a block diagram of an embodiment of the system of FIG. 1;
FIG. 3 is a block diagram of a processor in accordance with an embodiment of the present invention;
FIG. 4 is a block diagram of image measurements in accordance with an embodiment of the present invention;
FIG. 5 is a block diagram of parameter inputs in accordance with an embodiment of the present invention;
FIG. 6 is a block diagram of a measurement module of an imaging method in accordance with an embodiment of the present invention;
FIG. 7 is a block diagram of a modeling module of an imaging method in accordance with an embodiment of the present invention;
FIG. 8 is a block diagram of a data handling method in accordance with an embodiment of the present invention;
FIG. 9 is a block diagram of an image data analysis method in accordance with an embodiment of the present invention;
FIG. 10 is a block diagram of an image data display method in accordance with an embodiment of the present invention;
FIG. 11 is a block diagram of coordinate inversion of an image slide in accordance with an embodiment of the present invention;
FIG. 12 is a block diagram of outputs in accordance with an embodiment of the present invention;
FIG. 13 is a graph of specimen spot intensity over time;
FIG. 14 is a display of a frame of time-resolved specimen spot intensity;
FIG. 15 illustrates a TIFF image of time-resolved specimen spot intensity at a first time;
FIG. 16 illustrates a TIFF image of time-resolved specimen spot intensity at a second time;
FIG. 17 illustrates a differential TIFF image between the images shown in FIGS. 15 and 16; and
FIGS. 18 and 19 are histograms of the TIFF images shown in FIGS. 16 and 17.



Embodiments of the present invention and their advantages are best understood by referring to the detailed description that follows. It should be appreciated that like reference numerals are used to identify like elements illustrated in one or more of the figures. It should also be appreciated that the figures may not be necessarily drawn to scale.
DETAILED DESCRIPTION
The invention generally comprises a method and apparatus for acquiring, processing, and displaying data, and in one embodiment relates to acquiring, processing, and display of data from a two-dimensional arrangement of chemical substances obtained by an imaging technique and apparatus, such as that disclosed in U.S. Pat. No. 6,594,011, the contents of which have been previously incorporated by reference.
In one embodiment, a polarized light source of known polarization state is directed into an optical assembly, for example a total internal reflection member (TIR member), configured for a reflection at a light reflection surface, for example a total internal reflection surface (TIR surface), and then allowed to exit the optical assembly. In the context of this document, superposition of reflections as encountered at a layered optical structure where the layer thicknesses are smaller than the coherence length of the illuminating light is referred to as a single reflection.
The chemical specimen is in place above the light reflection surface in the evanescent field of the reflected light beam. After reflection, the beam is passed to a polarization-sensitive two-dimensional detector such as a polarizer and a camera or other types of detectors. The beam's content can then be processed to determine the change in polarization state, locally in the two-dimensional cross-section of the beam. This provides a spatially distributed map of change of polarization state in the specimen. A variety of techniques are available to determine the change in polarization such as measuring the deviation from a null condition or by comparing the input polarization state to the output polarization state.
The refractive index composition of the materials within the evanescent field determines the change in the polarization state of the beam due to the reflection at the light reflection surface. A two-dimensional variation of this composition within the light reflection surface is associated with a respective variation of the polarization state spatially distributed across the cross-section of the reflected light beam.
In one application, the chemical specimen forms a two-dimensional array of molecules (referred to herein as receptors and generally referred to as capture agents or affinity agents) with specific affinities towards respective other molecules (referred to herein as ligands). In this application, the invention is utilized to indicate the presence or absence or rate of binding between ligands and receptors on the array. Such arrays commonly consist of a plurality of discrete specimen spots. The present method and apparatus images the array so as to distinguish each of the discrete specimen spots represented by the local change in polarization state in the cross-section of the reflected beam.
Measurements are designed for maximum practical sensitivity and triggered at discrete intervals appropriate for the experiment, determined by a three-component analysis based on the affinity constants, size, and concentration of the analytes. Data is culled for conservation of computing and storage resources. If, for instance, it is known that the sample system contains low-affinity components, generally longer incubation or dwell time is required. If size of the analyte is small, maximum sensitivity settings of the instrument are required which in turn generally requires longer measurements and correspondingly longer intervals. If the concentration is low, such that a long incubation or dwell time is required, measurements will be timed accordingly so that excess data is not taken. If the reaction involves high affinity components, measurement intervals will be minimized, so that more data points are taken. Incubation and dwell time refer to the period of time in which the sample is in contact with the sensing array at nearly full concentration.
If the characteristics of the sample are unknown, an auto-tuning and data culling method is employed, in which binned low-spatial-resolution data is taken at moderate sensitivity settings and minimized intervals, the resultant differential images are analyzed for change, and once signals become evident or fail to become evident in a given time period, kinetic analyses of reactive areas are used to adjust measurement intervals, sensitivity, and spatial resolution to appropriate levels, while the data that displays no differential is discarded except for a few measurements, such as every fifth, tenth. If, for instance, the reaction becomes evident in the first ten seconds of incubation, measurement will proceed at maximal speed and moderate sensitivity for the duration, binning will continue to be employed and all data will be saved.
FIGS. 1 and 2 show an apparatus which implements one embodiment of the invention. As shown in FIG. 1, the apparatus 10 can be described conveniently as comprising three general portions. A first portion includes a polarized light source assembly 12, a second portion includes an optical assembly 14 providing a control layer and/or a light reflection surface, and a third portion includes a polarization-sensitive imaging detector assembly 16 which can employ for example a two-dimensional array detector.
Data from detector assembly 16 is sent by an electrical signal along a connector 24 to processor 18 such as a specially programmed computer and user access system including an image display. Data can be presented as an image, a data table, a graph, or in other forms. The polarized light source assembly 12 passes polarized light of known polarization state 20, which may be varied or varying to optical assembly 14 where a light beam reflection occurs. Reflected light 22, having a changed polarization state, passes to detector assembly 16, where it is recorded spatially over the cross-section of the beam. The recorded data is sent to processor 18 where the change of polarization state is determined to provide a spatially resolved map of changes in polarization state. Where the specimens are presented as an array of discrete spots, each spot will be imaged for its change in polarization state within the spot area.
FIG. 2 shows a more detailed schematic block diagram of one embodiment of apparatus 10. The polarized light source assembly 12 has a light source 26, a beam forming member 28 (if the nature of the light source is such as to make beam forming useful or necessary), a polarizer 30, and an optical retarder 32. In other embodiments, the light source may include a laser and a moving diffuser adapted to produce speckle-offsetting fluctuation of the minima and maxima in the speckle pattern caused by the laser. The moving diffuser may be attached to a mechanical actuator which is preferably a motor and servo-apparatus for providing the speckle offsetting fluctuations. The light beam then proceeds through the beam-forming element 28, the polarizer 30, and the optical retarder 32, exiting light source assembly 12 as light beam 20.
In this embodiment, the optical assembly 14 has an optical element 34 which has an optical surface 36. Also shown is a control layer 38 over optical surface 36, and between them an index matching substance 40. A specimen 42 is positioned on light reflection surface 39 of control layer 38 in one example. In an alternative optical arrangement, a control layer is placed above an index matching substance which in turn is placed above a flat optical member. However constructed, the invention incorporates an optical structure having a light reflection surface and the beam reflects at the reflection surface between entering and leaving the optical structure. In other words, there is a light reflection surface in optical contact with the specimen, such that the evanescent field associated with the total internal reflection interacts with the specimen.
In one embodiment, the post-reflection detector assembly 16 has a polarizer 44 and an imaging detector, for example a two-dimensional array detector 46 and preferably a camera of the CCD or CMOS array type. The post-reflection detector assembly 16 through which the beam 22 passes can alternatively consist of a polarizer member, a beam forming member, and an imaging detector such as a two dimensional array detector or other type of imaging detector.
The processor 18 is a specially programmed computer (or processor) and output means for processing the imagery into a representation of film thickness variations spatially resolved over the cross-section of the area imaged. The imaging is acquired by detecting changes spatially distributed in the local polarization state in the beam's cross-section caused by the total internal reflection. This provides information about the presence and composition in the array of substances on the substrate surface for each resolvable point on the surface. Different polarization state changes are included in the cross-section of the reflected beam indicative of the substances on the specimen in the location in the specimen array corresponding to a position in the detector.
Processor 18 receives the data as an electrical signal (on connector 24) and characterizes the change of polarization state spatially over the two-dimensional array. In processor 18, the analysis and processing is done in one embodiment by comparing the known polarization state of the incoming light from the light source assembly 12 with the changed polarization state of the reflected light 22, spatially resolved two-dimensionally within the beam which provides a map of spatially distributed points or spots in the specimen array. The polarization shift is then analyzed by processor 18 to provide information of the presence and properties of elements in the chemical specimen. Other known techniques, such as null processing can be used to determine the change in polarization state.
The processor can be a general or special purpose processor, preferably with network capabilities. It comprises a central processing unit (CPU), a memory, and a network adapter, which are interconnected by a main bus. Other conventional means, such as a display, a keyboard, a printer, a bulk storage device, and a read-only memory (ROM), may also be connected to the main bus. The memory may store network and telecommunications programs and an operating system (OS).
The invention as described above provides an extremely sensitive optical imaging system for real-time imaging of the binding status of biochip array elements on the surface of an optically transparent material such as a glass or plastic chip. An exemplary monitored array of a 15 mm square inscribed in a 20 mm circular field, with discrete specimen spots of size commensurate with the lateral resolution of the imaging optics, results in fully parallel, continuous real-time readout of up to 5 million sensor fields. Sensor sensitivity to surface attachment is in the femtogram/mm.sup.2 range (e.g., one DNA per square micron).
The apparatus of FIG. 1 operates by imaging the pattern of reactions on the biochip. Those reactions produce changes in the height, surface concentration, and/or refractive index of the material that reacts at each spot. The area imaged could be the entire biochip array or a portion of the entire biochip array. By providing an array of spots of different materials, different constituents in test material flowed over the spots bind in a manner which identifies those constituents. By including in a computer memory the positions of the various materials in the different spots of the array, the image produced by the apparatus of FIG. 1 identifies the constituents in the test material and can also determine the rate at which the reactions occur by imaging successively over time. With the apparatus described, height differences can be imaged dynamically over such short periods of time that intermediate height change readings can be recorded and therefore height change rates can be determined as well as allowing comparison of the rate of height change or intermediate amount of height change among the spots on the biochip array.
The processing and display of the image data by processor 18 will now be discussed in greater detail. Typically, microarray experiments have been analyzed at or near the approximate endpoint of reactions, which is presumed to be equilibrium, and have not provided real-time and/or time-resolved information. Endpoint analysis shows whether the experiment has worked or not but does not provide a way for real-time analysis and time-resolved analysis. Disadvantageously, such endpoint analysis does not allow for monitoring of the process under investigation, thus losing kinetic data, affinity data, and other time-resolved data regarding the process. For example, the present invention allows for the detection of time-related affinity data if certain molecules bind to a part of the array at the beginning of an experiment but the binding does not persist until the end of the experiment. Disadvantageously, endpoint analysis would not capture this type of data.
Such endpoint analysis also does not allow for modification or early termination of the experiment if an error occurs, thus wasting time and resources. For example, the present invention allows a user to change certain parameters to focus on an area of the array after viewing the progress of the experiments if so desired. Positive controls may be observed to verify that the chemistry and detection is working. In another example, if an air bubble or other system failure were to arise in the experiments and cause a significant error in the imaging or if the chemistry itself was to fail, the present invention's real-time and/or time-resolved imaging and display allows the user to stop the process and restart or modify the experiments or to correct the system failure. An endpoint analysis after full preparation and completion of the experimental process would be a waste of the precursor materials, money, time, and other experimental resources.
As noted above, in one embodiment, processor 18 includes a specially programmed computer (or processor) and display means for processing the image data in real-time into a representation of film thickness variations time-resolved and spatially-resolved over the cross-section of the area imaged.
FIG. 3 illustrates one embodiment of processor 18, which includes a data acquisition application 80 operably coupled to a data analysis application 82 which in turn is operably coupled to a data display application 85. Processor 18 further includes a parameter input interface 90 which is operably coupled to data analysis application 82. A browser 87 operably couples data display application 85 to a communication network, for example the Internet. A display device 89 is operably coupled to data display application 85 for displaying the graphical representations of the image data to a viewer. Both browser 87 and display device 89 are commercially available and known to those of ordinary skill in the art.
The image data may be presented in a hypertext markup language (HTML) format or any similar or succeeding similar language such as PHP: Hypertext Preprocessor (PHP), Active Server Pages, or Perl. This allows for ease of communication and sharing of the image display at remote locations through the Internet or other networking means via various display devices, such as PC display screens, personal digital assistants (PDAs), wireless telephones, and other mobile devices, as well as display near or proximate data acquisition application 80 as shown by dashed line 83.
Data from detector assembly 16 (FIG. 1) is sent along connector 24 in real-time and acquired by data acquisition application 80. The data outputted from data acquisition application 80 is sent along line 81 to data analysis application 82, where the data for multiple microarray spots is analyzed and normalized to quantify an intensity value and corresponding thickness value in real-time and over time (i.e., the data is time-resolved).
Output data from data analysis application 82 is sent along line 84 to data display application 85 which converts the output data into graphical representations for the viewer. In one embodiment, the intensity value is posted in a grid that represents the microarray itself and allows for display of the grid development in real-time and over time as will be explained in greater detail below.
Most microarray experiments include positive controls, negative controls, and/or dilutions over certain areas of the grid. Negative controls should not react during the experiments and are used to determine the background or baseline for the intensity measurements. Theoretically, positive controls and/or dilutions should produce reactions during the experiments and are therefore the brightest (or darkest depending on the display convention) areas of the image. Typically, positive controls on microarrays are set at the margins or other easily located positions, so that they may be used to determine a frame of reference or establish a reference direction, correct image aberration and distortion, or accomplish registration of images to be compared. According to an embodiment of the present invention, many controls are utilized so as to evaluate spot-to-spot variance. Advantageously, the present invention allows for instant feedback on the progress of a large number of experiments, ranging from 1 spot to about 50,000 spots, as real-time and time-resolved information about the microarray can be on display.
Data acquisition application 80 receives the image data from detector assembly 16 (FIG. 1) and can be used to not only receive the image data but to also run the imaging apparatus in one embodiment. In one example, with no intent to limit the invention thereby, data acquisition application 80 can comprise the software package IGOR commercially available from WaveMetrics, Inc. of Lake Oswego, Oreg., appropriately modified to be integrated with at least light source assembly 12 (FIG. 1), optical assembly 14 (FIG. 1), detector assembly 16 (FIG. 1), and data analysis application 82, for automatic data collection and retrieval.
FIG. 4 is a block diagram of an example of image measurements that may be collected and processed by data acquisition application 80 (FIG. 3) and sent to data analysis application 82 (FIG. 3) along line 81. Data acquisition application 80 receives raw images 101 taken at predetermined and/or user-selected time intervals “tn” and provides horizontal pixel location/coordinate “x”, vertical pixel location/coordinate “y”, and an intensity value “z” at the pixel coordinates x and y.
In one embodiment, ellipsometry analysis routines in data acquisition application 80 extract intensity values from the four images 102, 103, 104, and 105 at different polarizer positions (in phase modulation mode) and from these four readings determine the ellipsometric x and y value for each pixel in the image. This data is then fitted to a lookup table based on a selected optical model which results in a thickness map of x,y coordinates and thickness z.
In another embodiment, if nulling or off-null is used, the intensity map of an image at a fixed polarizer position (e.g., “direct” settings are in the IGOR control panel and allow these to be set) is fitted to a Jones or Mueller matrix optical model and a thickness map is generated. The unpolarized image is one of the four images used to generate x,y coordinates and is useful as a demonstration of the imbedded reflectometry measurement capabilities.
Referring back to FIG. 3, data acquisition application 80 outputs image data x, y, and z along line 81 to data analysis application 82 which then analyzes the image data substantially in real-time to produce spatially-resolved images in real-time and over time. Data analysis application 82 is able to evaluate and quantify values inside and outside of each spot in the array. In one example, at predetermined time intervals, the mean value of a spot and a local background value are selected as the parameters used to approximate an intensity value and a corresponding approximation of thickness over a spot normalized against aberrations such as drift and local noise. Thus, data analysis application 82 is able to quantify and qualify the microarray data from data acquisition application 80. In one example, with no intent to limit the invention thereby, data analysis application 82 can be the software package ImaGene commercially available from BioDiscovery, Inc. of El Segundo, Calif., appropriately modified to be integrated at least with data acquisition application 80, parameter input interface 90, and data display application 85 for data retrieval, analysis, and image processing.
Parameter input interface 90 is used to input parameters into data analysis application 82 via line 91. FIG. 5 is a block diagram of an example of parameter values that may be inputted into data analysis application 82 from parameter input interface 90 via line 91.
As shown in FIG. 5, parameters may be inputted for the following although not limited thereto: a physical model 110, a spot template construction 112, an optical model 116, assay conditions 114, and a thickness lookup table 118. Parameters for physical model 110 include but are not limited to the length, width, height, density, orientation, hydrophilicity profile, and affinity profile of the array. Parameters for spot template construction 112 include but are not limited to the number of subarrays, rows and columns, and spot identification. Parameters for optical model 116 include but are not limited to wavelength, angle, ambient refractive index (n) and extinction coefficient (k), layer of interest n and k, and media n and k. Parameters for assay conditions 114 include but are not limited to the media type, sample handling, temperature profiling, pump rate profiling, and measurement profile.
Referring now to FIG. 6, a block diagram is shown illustrating an example of a measurement module 120 of an imaging method that can be utilized by data acquisition application 80 and data analysis application 82. In step 121, six frames (a frame is a single still image from a dynamic series) per measurement are taken over timecourse t0 to tfinal. The raw data is processed in step 122 using ellipsometry calculations to calculate measured ellipsometric X values and measured ellipsometric Y values 123 and 124, respectively. The raw data also includes measured intensity values in step 125. Reference frames are designated and averaged in step 126 and then subtracted from the measurement frames in step 127. The final frame or the frame demonstrating the most change from the initial frame is processed in step 128 to flag spots which are oversized, undersized, and donut-shaped.
FIG. 7 is a block diagram illustrating an example of a modeling module 130 of an imaging method that can be utilized by data analysis application 82. Parameters to be entered for the physical model 131, for example a biolayer model, include but are not limited to the geometry (from molecular models, crystal structure), orientation, and multi-segment optical density assignment. Parameters for the optical model 132 include the n, k, and depth of ambient, substrate, functional layer, biolayer, and media. Wavelength and angle(s) of the light source is also entered. These modeling parameters are fit into a Beaglehole Multilayer Model 133 and/or an Evanescent Model 134. A lookup table 135 is created including ellipsometric x and y values versus thickness of the biolayer based upon the Beaglehole Multilayer Model. A lookup table 136 is also created including intensity versus thickness of the biolayer based upon the Evanescent Model.
FIG. 8 is a block diagram of an example of a data handling method 140 that can be utilized by data analysis application 82. A differential image is provided by subtracting a reference image (t0) from the latest (current) image (tn) in step 141. Such a differential image can advantageously show change with high resolution in real-time to a viewer when the image is displayed (see, e.g., FIGS. 15-17). A spot is then quantified in step 142 by various parameters including but not limited to a spot mean, median, and mode (MMM), a local background MMM, a spot size, and a spot qualitative score. The local background is then subtracted from the spot value in step 143. The spot value is then normalized to the background and the positive controls in step 144, thus controlling for drift noise or other experimental fluctuations. Finally, an affinity analysis may be conducted based upon the normalized spot value in step 145.
Table 1 below shows a table including possible output from data analysis application 82 but the present invention is not limited to such a list.








TABLE 1





Output
Definition







Field
Name of a field where the spot is located


Metarow
Number of metarow in the metagrid where the



spot is located


Metacolumn
Number of metacolumn in the metagrid where the



spot is located


Row
Number of row in the subgrid where the spot is



located


Column
Number of column in the subgrid where the spot



is located


GeneID
Gene ID information for the spot


Flag
Numeric code of the quality flag for the spot (0 -



no flag, flag codes 1, . . . , 7)


Signal Mean
Pixel intensity averaged over the local signal



region


Background Mean
Pixel intensity averaged over the local



background region


Signal Median
Median pixel intensity computed over the local



signal region


Background Median
Median pixel intensity computed over the local



background region


Signal Mode
Mode pixel intensity computed over the local



signal region (mode corresponds to the pick



location in intensity distribution)


Background Mode
Mode pixel intensity computed over the local



background region


Signal Area
Number of pixels in the local signal region


Background Area
Number of pixels in the local background region


Signal Total
Total pixel intensity summed over the local signal



region


Background Total
Total pixel intensity summed over the local



background region


Signal Stdev
Standard deviation of pixel intensities over the



local signal region


Background Stdev
Standard deviation of pixel intensities over the



local background region


Shape Regularity
First signal area of a spot is inscribed into a



circle. Than number of non-signal pixels that fall



within this circle is computed and divided by



circle's area. This ratio is subtracted from 1 and is



called “shape regularity”


Ignored Area
Area of ignored regions directly neighboring



(“touching”) the signal area is computed


Spot Area
Signal Area plus Ignored Area


Ignored Median
Median pixel intensity computed over the local



ignored region


Area To Perimeter
This quality measure defines spot's circularity.



Area of a spot is divided by a square of spot



perimeter and multiplied by π4. As a result, this



measure ranges from 0 (highly non-circular



shape) to 1 (a perfect circle)


Open Perimeter
Computes the proportion of signal perimeter that



touches the border of rectangular snip around the



spot


XCoord
X coordinate (in pixels) of grid circle



corresponding to the spot


YCoord
Y coordinate (in pixels) of grid circle



corresponding to the spot


Diameter
Diameter (in pixels) of grid circle corresponding



to the spot


Position Offset
Offset (in pixels) of the center of the grid circle



from the expected position in the grid


Offset X
X offset (in pixels) of the center of the grid circle



from the expected position in the grid


Offset Y
Y offset (in pixels) of the center of the grid circle



from the expected position in the grid


Expected X
X coordinate of expected position of the circle in



the grid. Expected position in the grid is



computed fitting least square lines to circle



centers in every row and column


Expected Y
Y coordinate of expected position of the circle in



the grid. Expected position in the grid is



computed fitting least square lines to circle



centers in every row and column


CM-X
X coordinate of the center of the mass of spot's



signal region


CM-Y
Y coordinate of the center of the mass of spot's



signal region


CM Offset
Offset (in pixels) of the spot's center of the mass



from the expected position in the grid


CM Offset-X
X offset (in pixels) of the spot's center of the



mass from the expected position in the grid


CM Offset-Y
Y offset (in pixels) of the spot's center of the



mass from the expected position in the grid


Min Diam
Diameter of the circle inscribed into the spot's



signal region


Max Diam
Diameter of the circle, the spot's signal region



can be inscribed in


Control
Name of a control type for current spot (no name



means the spot is not a control spot)


Failed Control
0 if the control passed all tests, 1 if at least one of



the tests failed


Background
0 if the spot passed background contamination


Contamination Present
test, 1 if it did not


Signal Contamination
0 if the spot passed signal contamination test, 1 if


Present
it did not


Ignored % failed
0 if the spot passed ignored percentage test, 1 if it



did not


Open Perimeter Failed
0 if the spot open perimeter test, 1 if it did not


Shape Regularity
0 if the spot passed shape regularity test, 1 if it


Failed
did not


Perim-To-Area
0 if the spot passed perimeter-to-area test, 1 if it



did not (see section 1.4)


Offset failed
0 if the spot passed offset test, 1 if it did not


Empty spot
1 if the spot was qualified as empty, 0 if it was



not


Negative spot
1 if the spot was qualified as negative, 0 if it was



not









Referring now to FIG. 9, a block diagram is shown illustrating an example of an image data analysis method 150 of the present invention. At step 151, each of the spots in the microarray are measured and the mean value of each spot is calculated using the measurement module. The modeling module is then called at step 153 to calculate thickness of the biolayer. The kinetic course of each spot is then calculated and plotted at step 155. Spot identification information is called at step 157 and image output tables and graphics are displayed in real-time and over time at step 159.
Referring back to FIG. 3, output from data analysis application 82, such as text files, XML files, or other appropriately formatted data, is sent via line 84 to data display application 85 which further processes the data for display. Data display application 85 includes commercially available database and spreadsheet programs such as Microsoft Access and Microsoft Excel which can receive data from data analysis application 82 and can then be manipulated by an algorithm for graphical representation of the data.
FIG. 10 is a flowchart of an example of an image data display method 160. The value of a spot is first calculated by subtracting a background value from the signal (step 161). The coordinates of the spot are retrieved, based upon quadrant A-D, row 1-12, and column 1-16 (step 163). Next, a color is generated according to a range such that change of thickness (shown through a change in color/contrast of the spot) is easily visible to the user (step 165). In one example, if the spot value is 8-bits, the image data display method of FIG. 10 assigns a gray scale value to every number between 0 and 4,096. If the spot value is 16-bits, a gray scale value is assigned to every number between 0 and 65,000. At the final step 167, the method inverts the y coordinate values for redisplay based on the viewer's perspective since the image view is from below the microarray in this example.
Table 2 below shows an example of software code for displaying time-resolved values of the ellipsometric z shift data, which is proportional to film thickness change, according to the method illustrated by the flowchart in FIG. 10.








TABLE 2







1:
<%


2:
Set Connl = Server.CreateObject(“ADODB.Connection”)


3:
MdbFilePath = Server.MapPath(“../private/maven.mdb”)


4:
Connl.Open “Driver={Microsoft Access Driver (*.mdb)};



DBQ=” & MdbFilePath & “;”


5:


6:
Set diff = Connl.Execute(“SELECT value FROM diff”&



Request(“n”) &“ ORDER BY field,row,column”)


7:
%>


8:


9:
<%


10:


11:
Function GenerateColor(NumberToConvert, MinValue, MaxValue)


12:


13:
  If NumberToConvert <= MinValue Then


14:
    GenerateColor = “#000000”


15:
    Exit Function


16:
  End If


17:


18:
  If NumberToConvert >= MaxValue Then


19:
    GenerateColor = “ftffffff”


20:
    Exit Function


21:
  End If


22:


23:
  Numerator = NumberToConvert − MinValue


24:
  Denominator = MaxValue − MinValue


25:


26:
  ScaledValue = Round(((Numerator * 255) / Denominator), 0)


27:
  GenerateColor = lCase(“#” &Right(“0” &



Hex(ScaledValue), 2) &Right(“O” &



Hex(ScaledValue), 2) &RightC‘O” &Hex(ScaledValue), 2))


28:


29:
End Function


30:


31:
%>


32:
<html>


33:
<head>


34:
<title>Maven</title>


35:
</head>


36:
<body bgcolor=“#000000”>


37:


38:
<table cellspacing=“0” cellpadding=“0” border=“0”



width=“100%” height=“100%”>


39:
<tr><td align=“center”>


40:


41:
<!-- main start -->


42:
<table cellspacing=“0” cellpadding=“10” border=“0”>


43:
<tr><td>


44:


45:
<!-- 1 start -->


46:


47:


48:
<table cellspacing=“20”>


49:
<%


50:
For Quadrant = 1 to 4


51:
  Select Case Quadrant


52:
    Case 1: QuadrantLetter = “C”


53:
    Case 2: QuadrantLetter = “D”


54:
    Case 3: QuadrantLetter = “A”


55:
    Case 4: QuadrantLetter = “B”


56:
  End Select


57:
%>


58:
  <%If Quadrant Mod 2=1 Then%><tr><%End If%>


59:
  <td>


60:


61:
  <table cellspacing=“4” cellpadding=“0” border=“0”>


62:


63:
<%


64:
  Set diff = Connl.Execute(“SELECT value FROM diff”&



Request(“n”) &“ WHERE Field = ‘” &



QuadrantLetter &“’ ORDER BY row,column”)


65:
  For Row = 1 To 12


66:
%>


67:
    <tr>


68:
<%


69:
    For Column = 1 To 16


70:
%>


71:


72:
<%


73:
‘ ranges for different slides


74:
‘ slide # = min,max


75:
‘00 = 0,0


76:
‘01= 4320,4900


77:
‘02 = 2660,3060


78:
‘03 = 10550,11000


79:
‘04 = 6220,6700


80:
‘05 = 1520,2200


81:
‘06 = 1240,1900


82:
‘07 = 60,500


83:
‘08 = 1630,2200


84:
‘09 = 90,700


85:
‘10 = 70,650


86:
‘11 = 90,650


87:
‘12 = 100,800


88:
‘13 = 3260,3900


89:
‘14 = 10890,11700


90:
‘15 = 7620,8500


91:
‘16 = 9630,10500


92:
‘17 = 12450,13500


93:
‘18 = 5970,6950


94:
‘19 = 7730,8920


95:
‘20 = 8490,9500


96:
‘21 = 8500,9500


97:
‘22 = 2580,3550


98:
‘23 = 10050,11000


99:
‘24 = 8000,8700


100:
‘25 = 6120,6720


101:
‘26 = 6360,7100


102:
‘27 = 6050,6800


103:
‘28 = 2600,3200


104:
‘29 = 6920,7500


105:
%>


106:
  <td



bgcolor=“<%=GenerateColor(diff(“value”),2600,3200)%>”><img



src=“cover.gif” width=“15” height=“15” alt=“”></td>


107:
<%


108:
    diff.MoveNext


109:
  Next


110:
%>


111:
<%


112:
    Next


113:
%>


114:
    </tr>


115:


116:


117:
  </table>


118:


119:
  </td>


120:
  <%If Quadrant Mod 2=0 Then%></tr><%End If%>


121:
<%


122:
Next


123:
Set diff = Nothing


124:
%>


125:
</table>


126:


127:


128:
</td></tr>


129:
</table>


130:
<!-- main end -->


131:


132:
</td></tr>


133:
</table>


134:


135:
</body>


136:
</html>


137:


138:
<%


139:
Set diff = Nothing


140:
Connl.Close


141:
Set Connl = Nothing


142:
%>









FIG. 11 is a block diagram of the coordinate inversion of an image slide noted above with respect to FIG. 10.
FIG. 12 is a block diagram of an example of outputs from data display application 85 which can be sent via lines 86 and/or 88 to browser 87 and display device 89, respectively. Outputs include but are not limited to real-time (live) displays, text files, and binary image files (x, y, and z values from IGOR). Real-time displays can include but are not limited to an initial image, a current image, a differential image, a thickness “map” which shows thickness over the microarray, spot “meters”, and a plot of thickness versus time. Text files can include but are not limited to spot information and related affinity information.
FIG. 13 is a graph of specimen spot intensity over time in seconds. Positive and negative controls are utilized to normalize the measured data as mentioned above. The graph demonstrates a steeper affinity slope, indicating fast interaction and more change, at the end of 75 minutes in the positive control 171 than in the other specimen spots, sample 173, and negative control 175. Correlation with labelled and conventionally scanned data is also demonstrated.
FIG. 14 is an example of an html display of a frame of time-resolved specimen spot intensity. In one example, each frame constitutes 78 kilobytes rather than the typical 600 kilobytes to 30 megabytes of the differential image. The data economy is thus demonstrated.
It will be apparent that FIGS. 13 and 14 are just two of a variety of graphical representations of the time-resolved image data which can be provided. In one example, time-resolved image data could be displayed in various tables, graphs, and charts.
For example, FIGS. 15-17 illustrate graphical representations of image subtraction, specifically subtraction of a reference image (FIG. 15) from each subsequent image (FIG. 16) in a time-resolved sequence of images, resulting in a “differential image” (FIG. 17) that may increase the practical sensitivity and dynamic range of the resultant image upon digitization. For example, if measurements can be made to seven significant digits, and a surface is monitored over time for small changes, but the surface already has irregularities such as gross features, roughness, or a tilt, much of the range of the resultant digitized image will be occupied by the “background” and not the data. 16-bit TIFF images are currently the most common and practical format for scientific imaging and analysis, due to dynamic range of the detection methods used to create them and the data storage considerations of larger bit-depth images. With 65,500 levels per pixel, if the roughness and tilt remain in the image, the small surface changes of interest will comprise only a tiny range within the image, and comparison to the reference image will reveal no discernable changes. However, if the differential image is generated before conversion to an image format such as a 16-bit TIFF, the full bit-depth of the image format is utilized for just the data of interest, rather than the background.
In FIGS. 15 and 16, a surface is measured at two different times, producing an initial and subsequent binary image. The initial image is subtracted from the subsequent image, producing the differential image in FIG. 17. All three images are then digitized into 16-bit TIFFs by identical means. A region of interest of the initial, subsequent, and differential TIFF images is displayed and analyzed. As can be easily seen in FIG. 17, a differential image of areas 181 and 182 show a change in the areas whereas a change is difficult to notice when visually comparing the individual binary images of FIGS. 15 and 16.
Referring now to FIGS. 18 and 19, the initial and subsequent images have a 10,000 count range, containing 40 distinct levels, while the differential image covers a 25,000 count range with 112 levels. The changes would be undetectable if comparing the post-digitization TIFF images.
Advantageously, the present invention allows for clear visualization of experimental progress in a microarray containing a plurality of specimen spots. A user interface with display device 89 is also within the scope of the present invention such that information regarding the graphical representations may be provided to the user at his request. For example, if the user were to position a pointer at a certain area of the graphical representation, actual data regarding the microarray, such as X and Y coordinates, thickness value, and gene ID of that sensing spot, could be displayed for the user.
The present invention also allows for ease of communication of a microarray's experimental progress outside of the laboratory to a plurality of parties. It is apparent that the present invention is not limited to displaying data on a single display device 89 (FIG. 3) but may be used to display data on a plurality of display devices using browser 87. Advantageously, such communication of the real-time and time-resolved image data allows for enhanced collaboration between researchers on experiments in a real-time setting. The data stream is smaller than would be required to transmit the images, which are at least 600 kilobytes.
The above-described embodiments of the present invention are merely meant to be illustrative and not limiting. It will thus be obvious to those skilled in the art that various changes and modifications may be made without departing from this invention in its broader aspects. For example, while communication channels within the figures, for example FIG. 3, have been referred to as lines, it should be understood that what are called lines can be buses capable of carrying a plurality of signals (either digital or analog as appropriate) in parallel or can even be wireless communication channels. Furthermore, although reference is made to biochips in the examples above, the procedure and the results apply generally to chemically sensitive materials on a light reflection surface. Therefore, the appended claims encompass all such changes and modifications as falling within the true spirit and scope of this invention.

## Claims

1. An apparatus for imaging, comprising:
a light source emitting a polarized light beam;
an optical assembly including a light reflection surface, wherein the light beam from the light source is reflected by the light reflection surface to provide an evanescent field adjacent the light reflection surface, the light reflection surface being adapted to allow placing thereon a specimen array such that the specimen array in the evanescent field causes spatially distributed polarization changes in the cross-section of the light beam;
a two-dimensional array detector positioned to detect the spatially distributed polarization changes caused by the specimen array; and
a processor operably coupled to the two-dimensional array detector, the processor processing data from the two-dimensional array detector to provide a two-dimensional representation of the spatially distributed polarization changes occurring in the specimen array in real-time.

2. The apparatus as in claim 1, wherein the specimen array comprises a two-dimensional array formed of multiple fields comprising biomolecular substances.

3. The apparatus as in claim 2, wherein the biomolecular substances are proteins, peptides, and/or polynucleotide sequences.

4. The apparatus as in claim 1, wherein the processor calculates an intensity value of a specimen array spot over time.

5. The apparatus as in claim 4, wherein the processor associates a color value to the calculated intensity value.

6. The apparatus as in claim 1, wherein the processor includes a display device for displaying the two-dimensional representation of the spatially distributed polarization changes occurring in the specimen array.

7. The apparatus as in claim 1, wherein the processor includes a browser application for uploading the two-dimensional representation of the spatially distributed polarization changes occurring in the specimen array to a network.

8. The apparatus as in claim 1, wherein the processor calculates an intensity value differential of a specimen spot in the specimen array.

9. A method of imaging, comprising:
passing a polarized light beam into an optical assembly including a control layer and a light reflection surface to provide an evanescent field with controlled height and intensity adjacent the light reflection surface, a specimen array in the evanescent field causing spatially distributed polarization changes in the cross-section of the light beam;
passing the reflected light beam out of the optical structure;
detecting the spatially distributed polarization changes caused by the specimen array; and
processing the detected spatially distributed polarization changes to provide a two-dimensional representation of the spatially distributed polarization changes occurring in the specimen array in real-time.

10. The method of claim 9, wherein the specimen array comprises a plurality of discrete specimen spots and the image is provided for each of the discrete specimen spots.

11. The method of claim 9, further comprising using the spatially distributed polarization changes to determine two-dimensionally distributed presence and/or properties of the specimen array constituents.

12. The method of claim 9, wherein the specimen array is in a micro-titer plate.

13. The method of claim 12, further comprising:
resolving the spatially distributed polarization changes for matching positions in the micro-titer plate; and
analyzing the polarization changes to determine desired characteristics in each position.

14. The method of claim 9, further comprising analyzing the polarization changes to determine the binding characteristics of each discrete specimen spot.

15. The apparatus of claim 1, wherein the processor is adapted to calculate at least one time-resolved value of the data from the detector including a thickness value of a specimen spot in the specimen array.