Patent Publication Number: US-8542899-B2

Title: Automatic image analysis and quantification for fluorescence in situ hybridization

Description:
CROSS REFERENCE TO RELATED APPLICATION 
     This application is a continuation of, and claims priority under 35 U.S.C. §120 from, nonprovisional U.S. patent application Ser. No. 13/199,412, filed on Aug. 29, 2011, now U.S. Pat. No. 8,391,575, which in turn is a continuation of, and claims priority under 35 U.S.C. §120 from, nonprovisional U.S. patent application Ser. No. 11/607,557, filed on Nov. 30, 2006, now U.S. Pat. No. 8,019,134. The entire subject matter of application Ser. Nos. 13/199,412 and 11/607,557 is incorporated herein by reference. 
    
    
     TECHNICAL FIELD 
     The present invention relates generally to locating specified image structures in digital images, and more specifically to a computer-implemented system for automatically identifying and quantifying cellular structures marked using fluorescence in situ hybridization (FISH). 
     REFERENCE TO ASCII TEXT FILE APPENDIX 
     This application includes an ASCII text file appendix containing source code to software that embodies the inventions described herein. The software code is algorithmic structure of a means for analyzing and quantifying marked cell components using a data network. The source code is in ASCII format. A portion of the disclosure of this patent document contains material that is subject to copyright protection. All the material on the ASCII text file appendix is hereby expressly incorporated by reference into the present application. The copyright owner of that material has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure, as it appears in the Patent and Trademark Office patent files or records, but otherwise reserves all copyright rights. The ASCII text file appendix includes one text file readable in the MS-Windows operating system. The file is named “FISH eCog converted XML.txt”, is 684 kilobytes large, and was created on Nov. 7, 2006. The file is an ASCII version of the XML code that generates the visual representation of FIGS.  17  and  26 - 28 . 
     BACKGROUND 
     Systems for detecting and analyzing target patterns in digital imagery have a wide variety of uses. One such use is analyzing anatomical regions in radiological images. For example, systems for analyzing computed tomography (CT) images are used for the computer-aided detection of cancerous regions in human breasts and lungs. Another use for such image analysis systems is to detect and analyze target patterns in biomedical images obtained from microscopes, such as confocal microscopes. For example, pathologists use confocal microscopes to analyze cells and their components, such as organelles, membranes, nuclei, genes, chromosomes and macromolecules such as RNA, DNA, proteins and peptides. Such image analysis is used not only in diagnosis and prognosis relating to medical patients, but also in basic research, drug discovery and clinical trials. 
     Confocal microscopy offers several advantages over conventional optical microscopy by providing a wider depth of field, eliminating out-of-focus glare, and allowing the collection of serial optical sections from thick specimens. The laser scanning confocal microscope (LSCM) is currently the most widely used confocal microscope for biomedical research applications. In the biomedical sciences, a major application of confocal microscopy involves imaging cells and cell components that have been labeled with biomarkers, such as fluorescent probes. Confocal microscopy in combination with in situ hybridization and fluorescence techniques can be used to study DNA and RNA sequences in chromosomes and to analyze cell components, such as chromosomes and genes. One such technique for analyzing cell components is Fluorescence in situ Hybridization (FISH). For additional information on the FISH technique, see U.S. patent application Ser. No. 11/050,035, published on Dec. 1, 2005 as Publication No. 2005/0265588 A1, by Gholap et al. (the entirety of which is incorporated herein by reference). 
     In one specific application, FISH is used to analyze the Her-2/neural gene in breast biopsies in order to provide a diagnosis and prognosis for breast cancer. Using confocal microscopy in combination with FISH, a pathologist calculates the degree of gene amplification as the basis for the diagnosis. In one accepted diagnostic procedure, the pathologist analyzes a minimum of one hundred nuclei in order to calculate the degree of amplification. In this conventional procedure, the pathologist manually counts the marked chromosomes and genes (called “fluorescence signals”) in each of the one hundred nuclei and then calculates the ratios of the genes to the chromosomes. A disadvantage of this conventional procedure is that even an experienced pathologist may miss some of the fluorescence signals due to fatigue and loss of concentration. Most of the biopsies contain normal counts of marked genes and chromosomes, and the pathologist may lose concentration with the tedium of counting genes and chromosomes in hundreds of nuclei in multiple biopsies. Moreover, determining whether a fluorescence signal represents a single gene or multiple overlapping genes based on the brightness and size of the fluorescence signal is often a subjective determination. Individual pathologists may have different counting styles. 
     Thus, an automated system for counting fluorescence signals obtained from the FISH technique is desired. Existing automated counting systems count fluorescence signals based on two-dimensional images. See, e.g., Gholap et al., Pub. No. 2005/0265588 A1, cited above. Even in existing systems that obtain three-dimensional information using confocal microscopy, however, the systems analyze two-dimensional images obtained by condensing the three-dimensional information, thereby losing much of the three-dimensional information. It is difficult to distinguish individual nuclei and other cell components in two-dimensional composite images obtained by condensing three-dimensional information. Fluorescence signals that touch or overlap other signals cannot be accurately counted. In addition, information concerning the distance between signals and the size of individual signals is lost. Thus, a system is sought for automatically counting fluorescence signals that are present in three dimensions in slides obtained using the FISH technique. 
     SUMMARY 
     An image analysis system extracts, segments, classifies, quantifies and counts three dimensional objects present in tissue, such as biopsy tissue of a breast cancer patient. The analysis system automatically analyzes and counts fluorescence signals present in the biopsy tissue marked using the Fluorescence in situ Hybridization (FISH) technique. The user of the system specifies classes of a class network and process steps of a process hierarchy. Then pixel values in image slices of the biopsy tissue are acquired in three dimensions. Each separate image slice of a z-stack is acquired at a different depth in the z-dimension of the biopsy tissue. A computer-implemented network structure is generated by linking pixel values of the image slices to objects of a data network according to the membership functions of the class network and the process steps of the process hierarchy. 
     Objects associated with pixel values at different depths of the biopsy tissue are used to determine the number, volume and distance between cell components. For example, the distance between genes and between a gene and the nuclear membrane can be determined. In one application, fluorescence signals that mark Her-2/neural genes and centromeres of chromosome seventeen are counted to obtain a diagnosis of breast cancer. Her-2/neural genes that overlap one another or that are covered by centromeres can be accurately counted. Signal artifacts that do not designate genes can be identified by their abnormal area or volume. 
     A method of automatically counting cellular components enhances the reliability and confidence of the FISH diagnostic technique. The method eliminates the human error associated with conventional manual diagnostic procedures using the FISH technique. Moreover, the method is more accurate than existing automated counting methods based on two-dimensional image analysis. The method enables the user quickly and easily to quantify the cellular components in hundreds of nuclei, in multiple regions of a slide, and in multiple slides of a biopsy. In addition, the method enables the analysis of slides from multiple biopsies. Consequently, the method delivers meaningful diagnostic support based on multiple biopsies, which cannot be provided by existing automated counting methods based on two-dimensional image analysis. 
     The method can also analyze images captured in multiple focal planes at multiple wavelengths using multiple biomarking techniques and spectral methods. For example, multiple images of the same biopsy tissue taken using a microscope, an X-ray device, a computer tomograph, an ultrasound imaging device, and a magnetic resonance imaging device can be analyzed and correlated. In addition, the same types of cell components in the various images can be labeled using different biomarkers. Objects that correspond to the same cell components in the various images are then linked, correlated, analyzed and counted. The diagnosis and prognosis of the patient is improved by correlating the results of the analysis of the various images taken using the different biomarkers and spectral analysis techniques. 
     In one specific embodiment, a software program receives a specification of a class network and a specification of a process hierarchy. Pixel values of an image that includes cell components marked using fluorescence in situ hybridization (FISH) are acquired. The software program then performs the process steps of the process hierarchy to generate a data network by linking selected pixel values of the image to objects. The objects are then classified according to the membership functions of each class and subclass of the class network. One of the classes corresponds to a particular type of marked cell component. The software program then counts the number of the particular type of marked cell component using the data network. 
     Other embodiments and advantages are described in the detailed description below. This summary does not purport to define the invention. The invention is defined by the claims. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The accompanying drawings, where like numerals indicate like components, illustrate embodiments of the invention. 
         FIG. 1  is a diagram illustrating the process of analyzing nuclei from biopsy tissue of a human breast. 
         FIG. 2  shows a slide containing the biopsy tissue of  FIG. 1 . 
         FIG. 3  is a diagram of multiple image slices taken from the slide of  FIG. 2 . 
         FIG. 4  is a diagram showing cell components in a nucleus from an image slice of  FIG. 3 . 
         FIG. 5  is a three-dimensional diagram of cell components that are to be counted. 
         FIG. 6  is a two-dimensional composite diagram of the multiple image slices of the three-dimensional diagram of  FIG. 5 . 
         FIGS. 7A-C  show actual microscopic images of nuclei, genes and centromeres that are counted by the analysis system according to the invention. 
         FIG. 8  is a microscopic images of nuclei containing green fluorescence signals that mark the centromeres of chromosome number seventeen and pink Her-2/neu fluorescence signals. 
         FIG. 9  is a schematic diagram representing part of a data network based on pixel values from the three image slices of  FIG. 5  that cut through the two nuclei. 
         FIG. 10  is a simplified schematic diagram of a computer-implemented network structure that includes a data network, a class network and a process hierarchy. 
         FIG. 11  shows digital image slices at various depths of a slide containing biopsy tissue. 
         FIG. 12  shows the red, green and blue image slice components that make up the image slices of  FIG. 11 . 
         FIG. 13  is a flowchart of steps for analyzing and counting cell components using the computer-implemented network structure of  FIG. 10 . 
         FIG. 14  is a diagram showing the class network of  FIG. 10  in more detail. 
         FIG. 15  is a flowchart showing the substeps of the first step of  FIG. 13  for specifying the class network of  FIG. 10 . 
         FIG. 16  is a diagram showing the process hierarchy of  FIG. 10  in more detail. 
         FIG. 17  is a screenshot of the graphical user interface of the analysis system containing an outline representation of the process hierarchy of  FIG. 16 . 
         FIG. 18  is a flowchart showing the substeps of the second step of  FIG. 13  for specifying the process hierarchy of  FIG. 16 . 
         FIG. 19  is a screenshot of a pop-up window generated by the analysis system to assist in specifying an algorithm in a step of  FIG. 18 . 
         FIG. 20  is a diagram showing representations of various types of links in the computer-implemented network structure of  FIG. 10 . 
         FIG. 21  is a simplified schematic diagram of the computer-implemented network structure of  FIG. 10  after the class network and process hierarchy have been specified in the specification mode. 
         FIG. 22  is a simplified schematic diagram of the computer-implemented network structure of  FIG. 10  after the data network has been generated in the execution mode. 
         FIG. 23  is a simplified diagram of a data network in which pixel values are linked to objects. 
         FIG. 24  is a simplified diagram of a data network in which objects are linked to other objects by various types of links. 
         FIG. 25  is a flowchart showing the substeps of the fifth step of  FIG. 13  for generating the data network of  FIG. 10 . 
         FIG. 26  is a screenshot of a graphical user interface generated by the analysis system to assist in the editing of the class network and process hierarchy of  FIG. 10 . 
         FIG. 27  is a screenshot of the graphical user interface generated of the analysis system with a window showing an outlined Her-2/neu gene in a nucleus. 
         FIG. 28  is a screenshot of the graphical user interface generated of the analysis system with a window showing the outline of what appears to be an Her-2/neu gene, but is actually an imaging artifact. 
         FIG. 29  is a flowchart showing the substeps of a step of  FIG. 25  for executing the process steps of the process hierarchy of  FIG. 10 . 
         FIG. 30  is a flowchart showing the substeps of a step of  FIG. 29  for generating a domain specified in a process step. 
         FIG. 31  is a simplified schematic diagram of a cognition network when the data network has been generated from many digital images, such as from many image slices of biopsy tissue. 
         FIG. 32  is a screenshot of a process hierarchy used by another embodiment of the computer-implemented network structure of  FIG. 10  to analyze individual cells in a cell assay. 
         FIG. 33  is a 3-dimensional diagram of a dividing cell output in the last step of  FIG. 13  with marked target objects. 
         FIG. 34  is a listing of high-level lines of XML code corresponding to a Cognition Language script that implements a class network and a process hierarchy for analyzing and counting fluorescence signals present in biopsy tissue marked using the FISH technique. 
         FIGS. 35A-F  show more lines of the XML code of  FIG. 34 . 
     
    
    
     DETAILED DESCRIPTION 
     Reference will now be made in detail to some embodiments of the invention, examples of which are illustrated in the accompanying drawings. 
     An analysis system is disclosed that automatically counts fluorescence signals present in biopsy tissue marked using the FISH technique.  FIG. 1  illustrates the process of analyzing nuclei from biopsy tissue  10  taken from a human breast  11 . First, the biopsy tissue  10  is extracted from one location in the breast  11  of the patient. Only one or just a few biopsy samples are taken partly because the biopsy procedure is painful. Taking many biopsy samples also damages the structure of the breast and is also typically avoided for both medical and aesthetic reasons. Under conventional analysis methods, only about one hundred nuclei of the biopsy tissue are manually analyzed. The novel automatic fluorescence signal counting system, however, enables the pathologist to analyze a very large number of nuclei and obtain a thorough understanding of the biopsy tissue. This is advantageous considering that only one biopsy tissue sample is typically taken from the breast  11 . Conventional manual analysis methods do not achieve the best diagnostic and prognostic results because only a small number of nuclei from a single biopsy tissue sample of the patient&#39;s breast are analyzed. The analysis system, however, is able automatically to count an arbitrarily large number of cell components. The biopsy tissue sample is sliced and made into many slides, for example, up to one thousand slides.  FIG. 1  shows the nth slide  12  of the one thousand slides. 
       FIG. 2  shows how the fluorescence signal counting system scans the biopsy tissue  10  on slide  12  at many locations. For example, the system can scan biopsy tissue on a typical slide at up to two hundred locations. At each location of the scans, the system generates multiple image slices at different depths of the z-axis. The multiple image slices are obtained using a confocal microscope. The stacks of image slices are called “z-stacks”.  FIG. 2  shows the top image slice  13  of a z-stack  14 . 
       FIG. 3  shows the many nuclei apparent in each image slice of z-stack  14 . Hundreds of nuclei are typically apparent in each image slice. For example, a non-cancerous nucleus  15  is one of the nuclei apparent in top image slice  13 . In this embodiment of the system that counts fluorescence signals present in breast tissue marked using the FISH technique, identifying the cell components within each nucleus is of primary importance. Therefore, only the membranes of the nuclei are shown in  FIG. 3 , as opposed to the cell membranes. 
       FIG. 4  shows certain cell components of a non-cancerous nucleus  15 , which has been stained with DAPI (4,6-diamidino-2-phenylindole). The cell components include centromeres and genes present on human chromosome number seventeen  16 . In the FISH technique, fluorescence signals are emitted by the marked cell components. In this embodiment that is related to the diagnosis of breast cancer, genes present on chromosome number seventeen are analyzed. The nucleus of a normal cell typically contains two copies of chromosome number seventeen. Genes that are to be analyzed are marked in the FISH technique with fluorescent probes. The marked genes then appear as brightly colored areas when viewed with a fluorescent microscope. Various parameters of the marked genes are then determined, such as number, size, shape, distance between the marked genes and distance between a marked gene and the nuclear membrane. In this embodiment related to the diagnosis of breast cancer, the FISH technique is used to analyze the Her-2/neural (Human epidermal growth factor receptor-2) gene in breast biopsy tissue in order to provide a diagnosis and prognosis for breast cancer. In cancerous cells of the human breast, a high degree of amplification of the Her-2/neu gene produces an overexpression of the corresponding protein. Thus, detecting an amplification of the Her-2/neu gene and a corresponding overexpression of the Her-2/neu protein is an indication of a poor prognosis for mammary carcinoma. The diagnosis of metastatic breast cancer from Her-2/neu overexpression is all the more useful because of the development of drugs that directly target the Her-2/neu protein and are specially suited to combat this type of cancer, such as Trastuzumab (Herceptin). These anti-cancer drugs are quite expensive. By better diagnosing this particular type of cancer, medical costs can be saved by administering these expensive drugs only to those cancer patients who have this particular type of cancer. In addition, by detecting the amplification of genes other than Her-2/neu, the analysis system supports the administration of personalized medication when new drugs are developed. Finally, personalized dosages based on a particular patient&#39;s biopsy tissue can also be administered. 
     The degree of amplification is determined by the ratio of the number of fluorescence signals from the Her-2/neu gene to the number of fluorescence signals that mark the centromere of each chromosome number seventeen on which the Her-2/neu genes are located.  FIG. 4  shows two copies of chromosome number seventeen  16 . In  FIG. 4 , each chromosome number seventeen  16  has two Her-2/neu genes and one centromere  17 . By convention, the Her-2/neu genes that are marked with the fluorescent probe LSI-HER-2/neu are made to appear pink or orange colored when viewed with a fluorescent microscope. The microscopic images are acquired in the gray scale and are then colorized using accepted conversions into the RGB scale for ease of viewing. Each centromere  17  of chromosome number seventeen that is marked with the fluorescent probe CEP-17 typically appears green.  FIG. 4  shows two green fluorescence signals  18 , each indicative of one copy of chromosome number seventeen  16 . A pink fluorescence signal  19  illuminates chromosome number seventeen  16  at each location of the Her-2/neu gene. In a non-cancerous cell, there is typically one Her-2/neu gene on each chromosome number seventeen  16 . The Her-2/neu gene is considered not to be amplified when each chromosome number seventeen  16  has only one Her-2/neu gene. The Her-2/neu gene is highly amplified where there are more than four Her-2/neu genes on each chromosome number seventeen  16 . 
     In one accepted diagnostic procedure, one hundred nuclei of a biopsy tissue sample are analyzed in order to calculate the degree of amplification of the Her-2/neu gene in the biopsy tissue sample. In each of the one hundred nuclei, the fluorescence signals from each Her-2/neu gene and each chromosome number seventeen are counted. The degree of amplification of the biopsy tissue sample is then categorized as being (i) not amplified, (ii) moderately amplified or (iii) highly amplified based on the following criteria. The sample is not amplified if less than ten percent of the nuclei have more than four signals  19  indicative of the Her-2/neu gene. The sample is highly amplified if more than ten percent of the nuclei have more than ten signals  19  indicative of the Her-2/neu gene. And the sample is moderately amplified if more than ten percent of the nuclei have both (i) more than four but less than or equal to ten signals  19 , and (ii) a quotient of signals  19  to signals  18  (indicative of chromosome number seventeen) of greater than two. For additional information on diagnostic procedures based on counting signals indicative of the Her-2/neu gene, see Pauletti et al., “Detection and quantitation of HER-2/neu gene amplification in human breast cancer archival material using fluorescence in situ hybridization,” Oncogene, 13:63-72, Jul. 4, 1996, which is incorporated herein by reference. For different types of cancer, and even for different types of breast cancer, the ranges for the degrees of amplification differ. 
     In another accepted diagnostic procedure for the type of breast cancer that responds to Trastuzumab (Herceptin), the fluorescence signals from each Her-2/neu gene and each chromosome number seventeen in one hundred nuclei are also counted. The ratio of Her-2/neu fluorescence signals  19  to chromosome number seventeen fluorescence signals  18  for each nucleus is then calculated. Finally, the average of the ratios is calculated. The pathologist uses the average of the ratios to develop a diagnosis of breast cancer. 
     There are, however, complicating factors that have hindered conventional counting methods from obtaining an accurate count of the number of Her-2/neu fluorescence signals  19  per nucleus. The novel automatic fluorescence signal counting system overcomes these complicating factors. For example, the analysis system operates as a computer program and is not prone to fatigue and loss of concentration. Moreover, the system recognizes when the components of a nucleus have already been counted and does not recount that nucleus, which would result in a double count. In addition, by recognizing which nuclei have already been counted, not-yet-counted nuclei are not missed. Most important, the system can determine whether a fluorescence signal represents a single gene or multiple overlapping genes. The system can also distinguish bright spots on the image slices that are artifacts and not fluorescence signals at all. 
       FIG. 5  illustrates how the three-dimensional nature of the cell components complicates the counting and can lead to incorrect results in conventional methods that count based on two-dimensional images and two-dimensional composites of three-dimensional information. The cells, nuclei and cell components of the biopsy tissue are present at different depths of the z-dimension in each slide. A fluorescence signal from a first gene that lies directly above a second gene in the z-dimension will overlap any fluorescence signal from the second gene. The signal from the second gene will go unnoticed in a two-dimensional image in the x-y plane. In addition, the signal from a centromere will cover up the signal from a gene that lies directly below the centromere. 
       FIG. 5  shows a nucleus  20  in a first cell  21 , as well as a nucleus  22  in a second cell  23 . Most of nucleus  20  of first cell  21  is at a higher depth in the z-stack than is nucleus  22  of second cell  23 . The analysis system has generated three image slices of z-stack  14  that cut through the nuclei of first cell  21  and second cell  23 . Nucleus  20  includes a first gene  24  that overlaps a lower-lying second gene  25 . 
       FIG. 6  illustrates how the cell components of first cell  21  and second cell  23  of  FIG. 5  would look when viewed from above in only two dimensions.  FIG. 6  shows a composite  26  of the image slices of  FIG. 5 . In this view, the Her-2/neu fluorescence signals  19  emanating from nucleus  20  partially overlap each other. Thus, from the x-y perspective, there are overlapping Her-2/neu genes  27 .  FIG. 6  also shows Her-2/neu genes  28  that are partially covered by a centromere. The analysis system is able accurately to count the Her-2/neu genes because the analysis system generates a data network based on the pixel values of multiple slices in the z-dimension. 
       FIGS. 7A-C  show actual microscopic images of nuclei, as well as genes and centromeres within the nuclei.  FIG. 7A  is a digital image acquired using a blue light channel to emphasize the stained nuclear membranes. Even using a blue light channel, it is difficult using conventional counting methods to distinguish the multiple overlapping nuclei from one another in  FIG. 7A .  FIG. 7B  is a digital image acquired using a red light channel to emphasize the pink Her-2/neu fluorescence signals  19 .  FIG. 7C  is a digital image acquired using a green light channel to emphasize the green chromosome number seventeen fluorescence signals  18 .  FIGS. 7B and 7C  illustrate the difficulty in using conventional counting methods to determine which Her-2/neu genes and which chromosomes number seventeen fall within each particular nucleus of  FIG. 7A . From the two-dimensional z-y perspective of  FIG. 7B , for example, it is difficult to determine the depth of each pink Her-2/neu fluorescence signal  19  and therefore to identify the nucleus to which each Her-2/neu gene belongs. 
       FIG. 8  shows actual microscopic images of nuclei containing green fluorescence signals  18  that mark the centromeres of chromosome number seventeen and pink Her-2/neu fluorescence signals  19 . The left most nucleus is from a non-cancerous cell. The nucleus has two green fluorescence signals  18  and two pink Her-2/neu fluorescence signals  19 . The two green signals  18  indicate the presence of two copies of chromosome number seventeen. The two pink signals  19  indicate the presence of two copies of Her-2/neu genes in the same nucleus. Thus, the ratio of Her-2/neu genes to chromosome number seventeen is 1.0, and the Her-2/neu gene is not amplified. The two nuclei on the right of  FIG. 8  are from cancerous cells; each has clumps of overlapping pink Her-2/neu fluorescence signals  19  that are difficult to distinguish from one another in the x-y perspective. The second nucleus from the right has three green signals  18  and approximately 13 pink signals  19 . The ratio of Her-2/neu genes to chromosome number seventeen is therefore approximately four, indicating that the Her-2/neu gene is highly amplified. 
       FIG. 9  is a diagram that represents part of a data network based on pixel values  29  of the three image slices of  FIG. 5  that cut through first cell  21  and second cell  23 . The pixel values of top image slice  13  that depict first gene  24  are linked to a first object  30 . The pixel values of a lower image slice  31  that depict second gene  25  are linked to a second object  32 . Both first object  30  and second object  32  are linked to a superordinated object  33 . By linking objects obtained from image slices at different depths of the z-dimension, additional information can be extracted from the biopsy tissue  10  than would be available by analyzing images of the tissue only from the x-y perspective. For example, a distance  34  between first gene  24  and second gene  25  can be determined. The distance  34  between first gene  24  and second gene  25  is also illustrated in  FIG. 5 . In addition, the volume of a cell component that intersects multiple image slices can also be determined. 
     Objects associated with pixel values on the same image slice can also be linked. Objects can be linked not only based on their relative positions on the image slice. For example, objects that represent similar nuclei can be linked, such as nuclei with similar areas, shapes or brightnesses. Nuclei can be linked based on their concavity or convexity, for example. This would permit all Her-2/neu genes located in nuclei having a similar shape to be linked. Then the analysis system performs a specific algorithm on all of the linked genes. In another example, the distance between nuclei in one image slice is determined by linking nuclei objects in that level. Where the distance is determined to be small because the nuclei are clustered, the analysis system can apply a more extensive algorithm in the z-dimension to separate and distinguish the nuclei from one another. In yet another example, the area or volume of a gene signal relative to the area or volume of the associated nucleus can be determined by linking objects from the same image slice as well as from different levels. 
     The novel automatic fluorescence signal counting system generates not only a data network based on pixel values of image slices, but also a class network and a process hierarchy. The class network defines the characteristics of objects that that will be classified as various cell components. The process hierarchy includes process steps that control the flow of the analysis and calculations performed on the pixel values and objects. 
       FIG. 10  is a simplified diagram of a computer-implemented network structure  35  used by the analysis system to count and analyze fluorescence signals obtained using the FISH technique. Network structure  35  is generated by the analysis system and an associated computer program. The associated computer program is called the Cognition Program. The network structure  35  includes a data network  36 , a class network  37  and a process hierarchy  38 . In the example of  FIG. 10 , data network  36  includes a first data table  39  and a second data table  40 . The table data values in data tables  39 - 40  are in the form of both numbers and text. 
     In this embodiment, some of the table data values are digital pixel values from image slices of biopsy tissue  10 , while other table data values describe the patient from whom the biopsy was taken. Thus, some of the table data values are floating-point values representing the spectral intensity of individual pixels of the image slices. The other table data values are items of metadata relating to whether the patient might have breast cancer. Examples of such information include the patient&#39;s gender, age, weight, height, blood values, prescribed medications, number of children, family history of ailments, whether the patient breast-fed her children, whether the patient smoked or used drugs. In  FIG. 10 , a first value  41  and a second value  42  are spectral intensity values from the image slices, whereas a third value  43  is an item of metadata, such as the weight of the patient. In this example, the pixel values of first data table  39  correspond to the top image slice  13 , and first value  41  corresponds to a pixel value of image slice  13  that depicts first gene  24 . Similarly, the pixel values of second data table  40  correspond to the next lower image slice  31 , and second value  42  corresponds to a pixel value of image slice  31  that depicts second gene  25 . 
     In this embodiment, network structure  35  is used by the analysis system to count nuclei and other cell components. The visual inspection of slides and the manual counting of cell components is time consuming and labor intensive. Because of the low prevalence of fluorescence signals from highly amplified Her-2/neu genes in most of the slides viewed by the pathologist, tedium can cause the pathologist to overlook highly amplified Her-2/neu genes when they are present. Network structure  35  and the analysis system that generates network structure  35  help the pathologist to avoid overlooking and miscounting Her-2/neu genes. 
       FIG. 11  is an example of image slices that are analyzed by network structure  35  and the Cognition Program. For example, the three image slices of  FIG. 11  are analogous to the three image slices of  FIG. 9 . The top image slice of  FIG. 11  corresponds to first data table  39 , and the middle image slice of  FIG. 11  corresponds to second data table  40 . In other embodiments, second data table  40  also includes metadata relating to the patient. Network structure  35  is used to identify and count cell components, such as nuclear membranes, centromeres and genes. To identify these three cell components, the analysis system filters out separate wavelengths of light that make up each image slice. The image data is typically acquired in a gray scale and then interpreted into an RGB scale by convention. Color schemes other than red-green-blue can also be used, for example, the hue-saturation-brightness (HSB) color scheme. For example, Her-2/neu fluorescence signals  19  could be interpreted as yellow instead of pink. In this example, nuclear membranes are most apparent in the gray scale corresponding to blue light; the marked centromeres of chromosome number seventeen are most apparent through a green filter; and the pink Her-2/neu fluorescence signals  19  pass through a red filter. Thus, for each image slice, the analysis system generates a pink image slice showing the Her-2/neu genes, a green image slice showing the centromeres of each chromosome number seventeen, and a blue image slice showing the membranes of the nuclei. The analysis system links the pixel values of the pink image slice to objects classified in the class hierarchy as genes. Pixel values of the green image slice are linked to objects classified as centromeres, and pixel values of the blue image slice are linked to objects classified as nuclear membranes. 
       FIG. 12  shows the red, green and blue image slice components that make up the image slices of  FIG. 11 . On the left of  FIG. 12 , three red image slices show pink Her-2/neu fluorescence signals  19 . In the middle of  FIG. 12 , green image slices show green fluorescence signals  18  indicative of chromosome number seventeen. On the right of  FIG. 12 , blue image slices show the membranes of the nuclei that contain the chromosomes with the Her-2/neu genes. 
     Returning to  FIG. 10 , data network  36  also includes objects and links. In this example, first value  41  is linked by a first link  44  to first object  30 . First object  30  in  FIG. 10  corresponds to first object  30  in  FIG. 9 . Second value  42  is linked to second object  32 . First object  30  is linked by a second link  45  to object  33 . Second object  32  is also linked to object  33 . Class network  37  includes a class  46 , a subclass  47  and a second subclass  48 . Class  46  is linked to subclass  47  and to second subclass  48 . In addition, class  46  of class network  37  is linked to object  33  of data network  36 . In this example, class  46  is the class for Her-2/neu genes. And subclass  47  is linked to second object  32 . In this example, subclass  47  is the class for Her-2/neu genes that are overlapped by other genes. Process hierarchy  38  includes a process step  49 . Process step  49  in turn includes a domain specification  50  and an algorithm  51 . Algorithm  51  is linked by a third link  52  to the third value  43  of first data table  39 . Domain specification  50  is linked by a fourth link  53  to the object  33 . Thus, an algorithm of a process step in process hierarchy  38  is linked to metadata in data network  36 , and a domain specification of a process step in process hierarchy  38  is linked to an object in data network  36 . 
       FIG. 13  is a flowchart illustrating steps  54 - 59  of a method by which the analysis system uses network structure  35  and the Cognition Program to perform computer-aided detection (CAD) of cell components that the analysis system then counts. In other embodiments described below, network structure  35  is used to detect objects other than cell components. The steps of  FIG. 13  will now be described in relation to the operation of network structure  35  of  FIG. 10 . 
     In first step  54 , a user of the analysis system specifies class network  37  by defining the likelihood that objects of data network  36  will belong to each particular class of class network  37 . The user of the analysis system is, for example, a research doctor who is applying his expert knowledge to train the analysis system in a specification mode. Such a research doctor could be a research pathologist working at a pharmaceutical company, for example. In addition to the research doctor, pathologists then also use the analysis system in an execution mode. 
       FIG. 14  shows class network  37  of  FIG. 10  in more detail. Class network  37  includes classes linked to subclasses that describe what the user expects to find in the image slices included in first data table  39  and second data table  40 . Thus, in this example, the classes and subclasses of  FIG. 14  describe what the user expects to see in the image slices of  FIG. 11 . The user starts by giving each class a name. In this example, the user has specified a background class  60 , an image border class  61  and a separate class for each of the N cells having a nucleus that is to be counted. For example, cell number one has a subclass  62  for the Her-2/neu genes of the cell that are marked with pink Her-2/neu fluorescence signals  19 . Cell number one also has a subclass  63  for green fluorescence signals  18  that mark the centromeres of chromosome number seventeen of the cell. The user has also given subclass  63  its own subclass  64  for those centromeres that overlap Her-2/neu genes. The user specifies a helper class to categorize cell components whose identity is unknown at the beginning of the analysis. 
     The user also specifies categories of metadata. In this example, class network  37  includes a class for patient data and subclasses specifying the types of patient data. The user has specified subclasses for the patient&#39;s age, weight, height, number of children, whether the patient breast-fed her children, the patient&#39;s family history of ailments, the patient&#39;s blood values  65 , and whether the patient smoked. 
     Each class may have an associated membership function that defines the probability that an object of data network  36  will belong to the particular class. The membership functions do not define whether an individual pixel value belongs to a class. Rather, each object is a group of pixels linked to the object, and the user specifies the membership function by defining the properties that the object must have to belong to the class. Examples of such properties include the area, shape, color and texture of the object. The area of an object may be determined, for example, by the number of pixels linked to the object. An item of metadata may also be a variable in a membership function. For example, the texture of an object that belongs to the class “nuclear membrane” may be different if the age and weight of the patient are over certain thresholds. 
       FIG. 15  is a flowchart that illustrates the substeps of step  54  of  FIG. 13  in more detail. In a substep  66 , a link type for a link between two classes or subclasses is specified. Links that are not specified in substep  66  can also be specified later in step  56  of  FIG. 13 . 
     In step  55  of  FIG. 13 , the user specifies process hierarchy  38  of  FIG. 10 . The user specifies not only the individual process steps, but also the order in which the process steps are to be executed in the execution mode of the analysis system. Thus, each process hierarchy has a root process step linked to other process steps. The process steps in turn may be linked to substeps. 
       FIG. 16  shows process hierarchy  38  of  FIG. 10  in more detail. Process hierarchy  38  includes a root process step  67  named “FISH 3D Analysis” with a domain specification  68  and an algorithm  69 . In this example, the user has specified four process steps  70 - 73  linked in a specific order to root process step  67 . The first process step  70  “FISH Mamma 2D” has a sub-process step  74  named “Image Border”. The third process step  72  “Link Objects, Slices, Nuclei and Signals” has four sub-process steps  75 - 78 , three of which have their own substeps. Substep  75  “3D Processes” has a first substep  79  named “Prepare Slices” and a second substep  80  “Classify Slices”. Substep  76  “Find Overlap” has a substep  81  named “Link Nuclei Using Overlap Calculation”. Substep  77  “Some Corrections” has a substep  82  named “Chromosome 17 Signal Overlapping Her-2 Signals”. 
     For each process step or sub-process step, the user has the option of specifying a domain and an algorithm.  FIG. 16  shows that the user has specified a domain  83  for the process step  72  and a domain  84  for the sub-process step  82 . The domain specifies classes that define the objects of data network  36  upon which the algorithm is to operate at run time in the execution mode.  FIG. 16  also shows that the user has specified an algorithm  85  for the process step  72  and an algorithm  86  for the sub-process step  81 . 
       FIG. 17  is a screenshot of a view of a graphical user interface generated by the analysis system. The screenshot includes a middle window containing an outline representation of the process hierarchy  38  of  FIG. 16 . Corresponding process steps from  FIG. 16  are labeled in  FIG. 17 . The substeps of subprocess step  74  have been expanded, and the substeps of the other process steps are hidden in this graphical user interface. The user can add and delete process steps from the process hierarchy  38  by using pull-down windows that appear in response to a right mouse click. 
       FIG. 18  is a flowchart that illustrates the substeps of step  55  of  FIG. 13  in more detail. In a substep  87 , the user specifies the domain of the process step that the user has created. In a substep  88 , the user specifies an object filter for the domain. For example, from the objects within the domain, the object filter passes to the algorithm all of those objects that are linked to fewer than sixteen pixel values. In a decision substep  89 , the analysis system queries the user as to whether the domain is navigational. The user is queried by a dialogue in a pop-up window. The domain is navigational when the objects to be operated upon are defined based on how they are linked to other objects. For example, a domain may include only those subobjects that are linked by a certain type of link to a parent objects. If the domain is navigational, in a substep  90  the user specifies the link types that define the vicinity of the parent object. If the domain is not navigational, in a substep  91  the user specifies an object container for the objects that are to be operated upon by the algorithm of the process step. For example, the object container can be all of the objects at a specified object level. The level of objects linked directly to table data values is referred to as object level zero. Objects linked directly to objects in object level zero are considered to be in object level one, and so forth. 
     In a substep  92  of step  55  of  FIG. 13 , the user specifies the algorithm that will operate on the objects specified in the domain. The user can choose preformulated algorithms from a database of algorithms accessed by the analysis system. For example, some algorithms are used for the segmentation of objects. Other algorithms are used for computation, such as for statistical calculations or to calculate the area of pixels linked to an object. 
       FIG. 19  shows a screenshot of a pop-up window generated by the analysis system to assist the user to specify the algorithm as described in substep  92 . 
     Returning to  FIG. 18 , in a substep  93 , the user specifies a break condition at which the algorithm stops operating on objects. For example, the algorithm may be iterative and operate on a group of objects a predetermined number of times, as defined by the break condition. 
     In step  56  of  FIG. 13 , the user then specifies various types of links. In network structure  35 , links can be between objects, between classes, and between process steps (collectively referred to here as nodes). In addition, there can be links between a class and an object, between a class and a process step, between a process step and an object, between a process step and table data, and between an object and table data. The links between a class and an object, between a process step and an object, and between an object and table data exit in network structure  35  only at run time during the execution mode of the analysis system. The user then uses the link types to define the relationship between the nodes of the class network and process hierarchy that the user specifies in the specification mode. In addition, the user uses the link types to define the relationship between the objects of the data network and the other nodes of network structure  35  that are to be generated at run time. 
       FIG. 20  shows representations of various types of links  94 - 103  in network structure  35 . The links describe the relation between the objects, classes and process steps. The most elementary types of links are either (i) exchange-relation links or (ii) relation links. Exchange-relation links describe an abstract, material or communicative exchange between nodes. Relation links, on the other hand, describe the relationship between nodes depending on relational contents. Where information is structured hierarchically, links are further subdivided into two groups. The first group links nodes at different hierarchy levels. The second group links nodes at the same hierarchy level. 
     Link  94  represents an exchange-relation link that connects nodes at different hierarchy levels. Link  94  represents the relationship between a larger, super-ordinated node A and a smaller, subordinated node B. Thus, link  94  represents a change in scale of information and denotes “B is part of A”. Links  95 - 97  are exchange-relation links that connect nodes in the same hierarchy levels. These links do not represent a change in scale of information and denote “B is an output quantity of A”. For example, the link  97  denotes “B is an attribute of A”. 
     Link  98  represents a relation link that connects nodes at different hierarchy levels and thus performs a scale change. Link  98  denotes “B in general is A”. Links  99 - 102  represent relation links that connect nodes in same hierarchy level. Link  100  denotes “A is locally adjacent to B”; link  101  denotes “A is similar to B”; and link  102  denotes “A is followed by B”. 
     Link  103  represents a link that connects nodes that are capable of carrying out certain operations on other nodes and links. For example, a node connected to link  103  can generate new nodes or links and can also delete a node or a link. Link  103  denotes “B is function of A”. For additional information on types of links in a semantic network structure, see U.S. patent application Ser. No. 11/414,000 entitled “Situation Dependent Operation of a Semantic Network Machine,” filed on Apr. 28, 2006, which is incorporated herein by reference. 
     Although in the embodiment of  FIG. 13  the link types are specified in step  56  after the class network and the process hierarchy are specified, in other embodiments the link types are specified before the class network and the process hierarchy are specified. 
       FIG. 21  illustrates the condition of computer-implemented network structure  35  in the specification mode after the user has specified class network  37  in step  54 , process hierarchy  38  in step  55 , and the link types in step  56 . In this example, in the specification mode the user has specified a link  104  between algorithm  86  and subclass  65  (Blood Values) of class network  37 . The user specifies link  104  by specifying that algorithm  86  determines which nuclei overlap one another depending on the blood values of the patient. In the specification mode, the user has also specified links  105  between domain specification  84  and subclasses of class network  37 , including a subclass  64  (Centromere Overlapping a Gene). The user specifies links  105  by specifying that domain  84  includes the objects that are determined in the execution mode to belong to subclass  64  and the analogous subclasses of the other cells. 
     In step  57  of  FIG. 13 , the analysis system acquires the values of first data table  39  and second data table  40 . In this example, the pixel values of the images of  FIG. 11  are generated by a confocal microscope. In other embodiments, the images are generated by an X-ray mammography device, a computed tomography (CT), an ultrasound imaging device, or a magnetic resonance imaging (MRI) device. The confocal microscope includes an image digitizer that converts the acquired images into digital images. In other embodiments, physical film of microscopic images is sent through a film digitizer to obtain the pixel values of the data tables. In yet other embodiments, the microscopic images are produced directly in digital format. The digital pixel values of the data tables indicate both the brightness levels and the color in the space domain of the images of  FIG. 11 . Thus, each image slice is captured using multiple wavelength channels, in this example corresponding to red, green and blue. Metadata values are also acquired in step  57 . In this example, some of the metadata is in text format, such as the identity of medication prescribed for the patient. Other metadata, such as the patient&#39;s weight, is in the form of a digital number. 
     In step  58  of  FIG. 13 , the analysis system runs in the execution mode and generates data network  36  by selectively linking table data values to objects according to the class network and the process hierarchy. While the classes of class network  37  describe what the user expects to find in the table data values, the objects reflect what the analysis system actually finds in the table data values. At run time in the execution mode, the analysis system executes the process steps as specified in process hierarchy  38 . Each object is generated by linking to that object pixel values having similar characteristics, such as brightness or the difference in brightness between a pixel and its neighbors. Thresholds of brightness of pixels that are associated together can be obtained from a gradient histogram of the pixel values in the digital image. The objects are then linked together into classes according to the membership functions of the classes. Thus, classes are linked to objects at run time. In addition, classes and process steps are linked to table data at run time. 
       FIG. 22  illustrates the condition of computer-implemented network structure  35  in the execution mode after the analysis system has generated data network  36 . Various classes of class network  37  have been linked to objects in data network  36  that belong to the classes. For example, the subclass  62  specifying a Her-2/neu gene of cell number one is linked by a link  106  to an object  107 , which in turn links pixel values of the image slice of second data table  40 . Similarly, subclass  62  of cell number one is linked by a link  108  to an object  109  that links pixel values of the image slice of first data table  39 . 
     In addition,  FIG. 22  shows that while the Cognition Program is running, links are also generated between classes, process steps, objects and table data. For example, object  107  representing pixel values of an Her-2/neu gene in the image slice of second data table  40  is linked by a link  110  to object  109  representing pixel values of the same Her-2/neu gene in the image slice of first data table  39 . Thus, the analysis system recognizes that the pixels values belonging to both object  107  and object  109  are associated with the same Her-2/neu gene. 
     Moreover, algorithms are linked to table data values. For example, algorithm  86  is linked by link  104  to class  65  (Blood Values) in the specification mode. In the execution mode, class  65  is linked by a link  111  to an object  112  for patient metadata. Thereafter in the execution mode, algorithm  86  is linked to an item of metadata  113  that contains a value representing the patient&#39;s blood values. Network structure  35  is shown in  FIG. 22  as a cognition network  114  when links are present between classes, process steps, objects and table data at run time in the execution mode. 
       FIG. 23  illustrates objects that have been linked to table data values having similar characteristics. In addition, objects are linked to other objects according to the membership functions that define the classes. The table data values of  FIG. 23  are arranged to illustrate that they are pixel values of a digital image. For example, one factor of a membership function is the area occupied by the pixels that make up the object. In one example, the area is calculated as being proportional to the number of pixel values linked to the object. 
       FIG. 24  illustrates objects linked to other objects in data network  36 . The objects are linked by the link types shown in  FIG. 20 . In the execution mode, an object that belongs to a class is linked to another object that belongs to another class when the two classes are linked together in class network  37 . 
       FIG. 25  is a flowchart that illustrates the substeps of step  58  of  FIG. 13  in more detail. In a substep  115 , the class network that is specified in step  54  of  FIG. 13  is loaded into a script execution engine of the Cognition Program. In a substep  116 , the process hierarchy that is specified in step  55  of  FIG. 13  is loaded into the execution engine. In a substep  117 , a data set N of the table data values acquired in step  57  of  FIG. 13  is loaded into the execution engine. 
     In a substep  118  of step  58  of  FIG. 13 , the process steps specified in step  55  of  FIG. 13  are executed on the data set N. In substep  119 , the user has the option to run the Cognition Program in an interactive mode. In the interactive mode, the results of the computer-aided detection are displayed to the user, such as a research doctor. If the user is not satisfied with the results, the user can edit the classes of class network  37  or the process steps of process hierarchy  38  and immediately re-execute the process steps on the data set N. The user can edit the process steps using the graphical user interface and the script editor of the Cognition Program. 
       FIG. 26  is a screenshot of one view of the graphical user interface generated by a view module of the Cognition Program. The screenshot includes a window containing three image slices (top, middle and bottom) at three successive depths of in the z-dimension. The image slices show cell nuclei. The user can edit the class network  37  and the process hierarchy  38  using the windows on the right of the screenshot so that the target region recognized by the particular process step being edited is satisfactory. For example, by right mouse clicking on a process step in the lower right window, a pup-up window appears with a dialogue asking the user whether he wishes to add a sub-process step or append a process step below the clicked process step. The user is then asked to choose a domain and an algorithm for the new process step. Existing process steps can also be edited. 
     The user can also add or edit classes using the upper right window. A class is also added by right mouse clicking and responding to the queries in the pop-up window. The user is asked to name the new class and enter properties of objects that belong to the class, such as color, area, asymmetry, density and the angles along the border of the object. Thus, the Cognition Program can also analyze color digital images. In this embodiment of the analysis system that automatically counts fluorescence signals present in biopsy tissue marked using the FISH technique, the Cognition Program analyzes images slices acquired using red, green and blue color channels as shown in  FIG. 12 . In the image slice shown in the graphical user interface in  FIG. 26 , however, the colors of the nuclei do not correspond to the spectral colors used to acquire each image slice. Instead, the user has assigned each nucleus to a different class. Then, for ease of viewing, the user has assigned a different color to each class that is shown on the graphical user interface. 
     As part of creating a class, the user also defines a membership function for objects that belong to the class. For example, the user can define an “asymmetry function” as part of the membership function. The asymmetry function describes the shape of the pixels that make up an object by approximating an ellipse. For example, the user can use the asymmetry function to classify nuclei objects. The numerator of the asymmetry function describes the long axis of the ellipse, and the denominator describes the short axis. A shape of pixels that approximates a circle has an asymmetry value of one. An elongated shape of pixels has an asymmetry value much greater than one. The user can also define a “density function” to classify nuclei objects. The density function is the square root of the area of the pixels divided by the length of the border around the pixels that comprise the object. The asymmetry function and the density function can be used in the diagnosis of breast cancer. The shape of a nucleus in a cancerous cell is different from the shape of a nucleus in a normal cell. 
       FIG. 27  is a screenshot of another view of the graphical user interface generated by the view module of the Cognition Program. The screenshot includes a window on the left showing a portion of an image slice in which an Her-2/neu gene in a nucleus has been outlined. A window on the right provides information about each Her-2/neu gene in the image slice, including the outlined Her-2/neu gene. For example, the analysis system indicates that the outlined Her-2/neu gene has an area of nineteen pixels. The analysis system also indicates the x-y coordinates of the outlined Her-2/neu gene within the image slice. 
       FIG. 28  is a screenshot of yet another view of the graphical user interface showing what appears to be an outlined Her-2/neu gene in the window on the left. A window on the right provides information about the outlined object. In this example, the analysis system indicates that the outlined object has an area of 582 pixels. Through the membership function of the class for Her-2/neu genes, the analysis system determines that the object is too large to be produced by an Her-2/neu fluorescence signals  19 . Therefore, the analysis system determines that the object is not an Her-2/neu gene, but rather an imaging artifact. As in  FIG. 27 , the analysis system indicates the x-y coordinates of the outlined artifact. From the x-y coordinates, the analysis system determines that the Her-2/neu gene of  FIG. 27  lies under and is covered by the artifact of  FIG. 28 . Nevertheless, the analysis system is able to identify the Her-2/neu gene of  FIG. 27 . 
     Because class network  37  and process hierarchy  38  are specified using a Cognition Language (CL) based on the XML script language, class network  37  and process hierarchy  38  can be edited without recompiling the Cognition Program. Thus, the user can input a new membership function of a new class at run time that defines whether the objects of data network  36  will belong to the new class, and the process steps can be performed immediately on the newly generated data network  36  without recompiling the program instructions of the Cognition Program. The XML-based Cognition Language and the graphical user interface allow the user to more quickly “train” cognition network  114  to recognize Her-2/genes marked by fluorescence signals  19  and centromeres of chromosome number seventeen marked by fluorescence signals  18 . The ability to edit the class network  37  and process hierarchy  38  at run time differentiates the Cognition Program from conventional CAD schemes that cannot change the process of applying rules once the CAD scheme begins analyzing a particular digital image. After the user of the Cognition Program determines that the results of the pattern recognition performed on a data set N are satisfactory, the process steps are automatically executed on the next data set N+1. The Cognition Program can then automatically perform the process steps on a large number of data sets, for example by performing the processing overnight. Reports are generated for each level of data, such as for all nuclei, for each image slice, for each z-stack and for each slide. 
     The Cognition Program would typically not be run in the interactive mode when the user is not a research doctor but rather a pathologist who is analyzing a new patient&#39;s biopsy tissue. A pathologist would use the Cognition Program with a class network and a process hierarchy that have already been trained by the research doctor. In that case, all of the process steps of process hierarchy  38  would be executed on all of the data sets, and the results would be saved for displaying as the final results in step  59  of  FIG. 13 . 
       FIG. 29  is a flowchart that illustrates in yet more detail additional substeps of substep  118  of  FIG. 25 .  FIG. 29  illustrates the process by which each process step of process hierarchy  38  operates on objects specified by the domain. In a substep  120 , the domain that was specified in substeps  87 - 90  of  FIG. 18  is generated. In a substep  121 , the execution engine retrieves the next object of the domain that is to be operated upon. In a substep  122 , the execution engine executes the algorithm of the process step on the retrieved object. In a substep  123 , the execution engine executes the algorithm of any sub-process steps on the retrieved object. In a substep  124 , the execution engine retrieves the next process step of the process hierarchy so that substeps  120 - 123  can be repeated for the domains and the algorithms of the next process step and sub-process steps, if any. 
       FIG. 30  is a flowchart that illustrates in yet more detail additional substeps of substep  120  of  FIG. 29 .  FIG. 30  illustrates the process by which the domain that was specified in substeps  87 - 90  of  FIG. 18  is generated at run time. 
     Returning to a final step  59  of  FIG. 13 , the Cognition Program outputs the final results of the computer-aided detection based on the cognition network  114  that was generated using class network  37  and process hierarchy  38 . 
       FIG. 31  shows cognition network  114  of  FIG. 22  when data network  36  has been generated from many data tables, each containing a digital image. Thus,  FIG. 31  is a more detailed example of the diagram of  FIG. 9  in which a data network is generated based on pixel values from multiple image slices. By generating data network  36  from digital images obtained from many parallel planar slices of biopsy tissue, for example, the Cognition Program detects Her-2/neu genes in three dimensions within the biopsy tissue. 
       FIG. 31  illustrates that in the specification mode a domain specification is linked by a link  125  to a class. In the execution mode, the Cognition Program acquires table data values comprising the many digital images that are slices of a three-dimensional data set. The Cognition Program then applies the membership function of the class to the values of each of the digital images and determines that various objects generated from the many digital images belong to the class. For example, the Cognition Program determines that each of objects  126 - 131  from digital images in data tables  132 - 136 , respectively, belongs to the class. The class is then linked to each of the objects  126 - 131 . For example, a link  137  links the class to object  126 , which in turn is linked to pixel values from a first digital image in data table  132 . At run time, the domain specification is then also linked to the objects that belong on the class specified in the domain specification. For example, a link  138  links the domain specification to the object  126  while the Cognition Program is running. This allows the algorithm of the process step to operate on all of the objects that comprise the 3-dimensional object, in this example an Her-2/neu gene. Finally, each of the objects  126 - 131  that belong to the class and that are generated from the many digital images are linked to each other in data network  36 . For example, object  126 , which is linked to pixel values from the first digital image, is linked by a link  139  to object  127 , which is linked to pixel values from the second digital image. Because all of the objects  126 - 131  are identified as belonging to the same class, the physical characteristics of the class can be determined. For example, where the class is a gene clump or a nucleus, the analysis system can determine the volume of the gene clump or nucleus. 
       FIG. 31  also illustrates that the Cognition Program has linked an object generated from one image slice to two objects in an adjacent image slice. Object  129  that is generated from the fourth image slice is linked to two objects of the same class generated from the fifth image slice. Object  129  is linked by a link  140  to object  130  and by a link  141  to a second object  131  from the fifth image slice. In this way, the Cognition Program is able to detect 3-dimensional objects such as blood vessels that fork into multiple portions in adjacent image slices. 
     Linking objects in multiple scans can also be used to track movement over time. Instead of the scans representing adjacent physical planes of a physical object, multiples scans are analyzed that are acquired at different times. In one example, the objects  126 - 131  belong to biopsy tissue samples from the same patient that are taken at one-month intervals. The change in shape in the nuclei and the change in amplification of the Her-2/neu genes is used to provide a prognosis of the patient&#39;s condition. In another example, the objects  126 - 131  belong to the class representing a cell. Digital images are taken of the cell at different time intervals in minutes. Movement can be tracked by linking objects of the same class that are obtained from digital images taken at adjacent time intervals. Over the four time intervals at which the digital images of data tables  132 - 135  are taken, the cell described by the class linked to objects  126 - 129  grows from four pixels to seven pixels. Then after the fifth time interval, the cell divides into object  130  with four pixels and object  131  with four pixels. The movement and change in shape of cells and cell components need not be tracked in adjacent time intervals, but rather can be analyzed at irregular times. Movement of three- or N-dimensional objects can also be tracked. In one example, the fourth dimension analyzed is time, and the fifth dimension is speed (change in time). 
     In another embodiment, the Cognition Program acquires the multiple digital images from a video movie instead of from multiple scans. For example, the video movie depicts movement of a bacterium, a cell or an interphase nucleus. The Cognition Program can be used to detect one moving cell from among multiple moving cells. 
     In yet another embodiment, the analysis system analyzes and correlates images acquired using different imaging and marking methods. For example, data tables  132 - 135  include images of the same biopsy tissue taken using a microscope, an X-ray device, a computer tomograph, an ultrasound imaging device, and a magnetic resonance imaging device. Thus, the analysis system provides a multi-modal display of images obtained from multiple spectral imaging techniques. The multi-modal images are correlated to one another using the graphical user interface of the analysis system. In addition, the various images can be taken using different biomarkers, such as FISH, chromogenic in situ hybridization (CISH) and polyclonal antibody (NCL-Ki67p) labeling of the Ki67 antigen. Thus, each image of the multi-modal display shows multiple biomarkers. Images can also be taken using “multiplex” biomarkers that mark different cell components in different ways. In addition, images of marked proteins, such as estrogen and progesterone, can also be displayed and analyzed. Objects that correspond to the same marked cell components in the various multi-modal images are then linked in data network  36 . Diagnoses and prognoses can be improved by correlating the results of analyzing the various images taken using different biomarkers and spectral analysis techniques. 
       FIG. 32  is a screenshot of a process hierarchy in another embodiment of cognition network  114  that analyzes individual cells in a cell assay. Three-dimensional properties of the cells are analyzed using one hundred scans at different depths of an individual cell using a confocal microscope. During the “training” process when the Cognition Program is run in the interactive mode as described by the substeps of  FIG. 25 , the process hierarchy of  FIG. 32  is presented to the user in the lower right window of  FIG. 26 . 
       FIG. 33  shows the output of step  59  of  FIG. 13  as presented to the user on the graphical user interface for the embodiment of  FIG. 32 . Two 3-dimensional cells from a cell assay are depicted in  FIG. 33 . In the image of  FIG. 33 , target objects  142  that belong to the same class are displayed with the same color. In this example, target objects  142  are marked mitochondria. The Cognition Program compares the mean volume of the marked mitochondria to the volume of surrounding cytoplasm. 
     In yet other embodiments, cognition network  114  analyzes cells that are in various forms of aggregation. Individual cells in wells in plates of a cell-based assay can be analyzed. Grouped cells in a tissue formation assay can be analyzed. Tissue biopsy samples can be analyzed as described above. And tissue micro arrays containing different types of tissue can be analyzed. A tissue micro array may, for example, include tissue from the skin, breast, lungs and heart that exhibits different types of cancer. In this example, the analysis system is used to correlate the responses of the different cancer types in the different tissues to particular dosages of drugs. Thus, the analysis system is used in pharmaceutical research to analyze tissue micro arrays. In the method of  FIG. 13 , table data values are acquired in step  57  from images of cell tissue in multiple wells of a tissue micro array. The Cognition Program is used to look for morphological changes in the cells. The Cognition Program is used to detect motion in the cell tissue by analyzing multiple images taken of the same well after successive time intervals. The Cognition Program determines how long it takes for the cells of the tissue to stop dividing when a specified dosage of a drug is placed in the well. 
       FIG. 34  is a listing of high-level lines of XML code that corresponds to a CL script that implements a class network and a process hierarchy for automatically counting fluorescence signals present in biopsy tissue marked using the FISH technique. The CL script was created and edited using a graphical user interface similar to the one shown in  FIG. 26 . All of the lines of the XML code are present in an XML file entitled “FISH eCog converted XML.txt” and contained in the CD Appendix. 
       FIGS. 35A-F  show more lines of the XML code of  FIG. 34 . The XML description of selected classes of  FIG. 14  and process steps of  FIG. 16  are identified by XML comments in  FIGS. 25A-F . For example,  FIG. 35A  shows an XML description  143  of the class “Cells” of  FIG. 14 . The class “Cells” is identified with the class ID of “7”. In addition,  FIG. 35A  shows an XML description  144  of a Helper class of  FIG. 14  labeled as “potential Her2/neu”. The Helper class is a temporary class and generates intermediate objects at run time. In addition to the Helper class that is specified by the user, the analysis system also employs dynamically generated classes. These classes are generated at run time and are deleted before the final result of classification is achieved. Intermediate objects are linked to the Helper class and to the dynamically generated classes. The intermediate objects are reclassified as the Cognition Program iteratively performs the process steps to optimize the categorization of objects into the remainder of the specified classes. Thus, performing the process steps of the process hierarchy is an adaptive process that is repeated and optimized on same digital image. 
       FIG. 35D  shows an XML description  145  of the domain specification of a sub-process step of the sub-process step  70  (fish mamma 2D) of  FIG. 16 . The class ID “7” for the class “Cells” is listed under the list of classes &lt;lClss&gt; of the domain specification. The class ID in the domain specification generates a link between the domain specification and the class at run time. At run time, links are also generated from the domain specification of the sub-process step to the actual objects of the data network that are determined to belong to the class “Cells”. 
     The analysis system can also be applied on stains and biomarkers other than those that mark the Her-2/neu gene, such as IHC, CISH and Ki-67. Correlations between results from these other biomarkers and those from FISH can be performed on a single specimen or tumor patient. Such an application is useful in applications of Translational Medicine and in a “Case Based Reasoning” method. Results from the analysis system can also be correlated to radiology image data in order to obtain a multiscale, multiresolution and multimodal computer-aided diagnosis. The disclosed method allows a user to correlate different image analysis results, such as between morphological and molecular pathology and between pathology and radiology. In addition, results at different clinical stages can be correlated, such as between the time of analysis and the time of treatment. In this way, detailed knowledge about the extracted objects, their mutual relationships and the entire tissue or tumor are generated. 
     The analysis system performs computer-aided detection (CAD) of cell components in combination with a work station. The Cognition Program runs on the work station. For faster computation and analysis, an on-chip solution incorporates the process steps into hardwired processing units of an application specific integrated circuit (ASIC) or a programmable logic device (PLD). The analysis system can also be used in conjunction with “virtual microscopy” in which automated analysis of slides is performed without manual involvement. Knowledge is extracted from a large amount of analyzed data that is acquired over many hours or days. The analysis system is used to recognize patterns and relationships in the large amount of data. For example, the analysis system recognizes patterns in the distances between nuclei containing multiple marked Her-2/neu genes and patterns in the shapes of marked Her-2/neu genes. 
     Although the present invention has been described in connection with certain specific embodiments for instructional purposes, the present invention is not limited thereto. For example, although embodiments of the Cognition Program and computer-implemented network structure have been described above in relation to the computer-aided analysis and counting of fluorescence signals present in biopsy tissue marked using the FISH technique, the Cognition Program and network structure can equally be applied to detecting and analyzing target patterns in other microscopic images. In addition to analyzing images acquired with conventional confocal microscopy, microscopic images acquired in the infrared light band can also be analyzed. The Cognition Program and network structure can also be used to detect and analyze anatomical regions such as the human brain, lungs and breasts, as well as microorganisms, non-living cells and the cells of plant. Thus, the analysis system can be used in environmental applications. Accordingly, various modifications, adaptations, and combinations of various features of the described embodiments can be practiced without departing from the scope of the invention as set forth in the claims.