Scanned image alignment systems and methods

Abstract

Systems and methods for aligning scanned images are provided. A pattern is included in the scanned image so that when the image is convolved with a filter, a recognizable pattern is generated in the convolved image. The scanned image may then be aligned according to the position of the recognizable pattern in the convolved image. The filter may also act to remove the portions of the scanned image that do not correspond to the pattern in the scanned image.

1 . An array comprising one or more array information features.  
   
   
       2 . The array of  claim 1 , wherein said one or more array information features comprises at least  4  features.  
   
   
       3 . The array of  claim 2 , wherein said features are positioned in a defined pattern on said array.  
   
   
       4 . The array of  claim 3 , wherein said defined pattern provides a symbol when specifically bound to target.  
   
   
       5 . The array of  claim 1 , wherein said one or more features provides coded information when specifically bound to target.  
   
   
       6 . The array of  claim 5 , wherein said coded information is binary or non-binary coded information.  
   
   
       7 . A method for providing information about an array, said method comprising: contacting an array of  claim 1  with a sample comprising a target that binds to at least one of said one or more information features to produce at least one signal that provides information about said microarray.  
   
   
       8 . The method of  claim 7 , wherein said target is spiked into said sample prior to contacting of said array with said sample.  
   
   
       9 . The method of  claim 7 , wherein said information is provided by assessing binding of said target to said one or more array information probes.  
   
   
       10 . The method of  claim 9 , wherein said assessing is by determining the presence, absence or level of binding to control levels of binding.  
   
   
       11 . The method of  claim 7 , further comprising determining the presence, absence or level of at least one signal that provides said information.  
   
   
       12 . The method of  claim 11 , wherein said at least one signal provides a binary code, where 0 is represented by no detectable signal and  1  is represented by a detectable signal.  
   
   
       13 . The method of  claim 11 , wherein said at least one signal provides a binary code, where  1  is represented by no detectable signal and 0 is represented by a detectable signal.  
   
   
       14 . The method of  claim 11 , wherein said at least one signal provides a binary code, where 0 is represented by a signal generated by a first label and  1  is represented by a signal generated by a second label that is detectably distinguishable from the first label.  
   
   
       15 . The method of  claim 7 , further comprising determining a level of said at least one signal to provide a non-binary code that provides said information.  
   
   
       16 . The method of  claim 15 , wherein said non-binary code is represented by levels of signal relative to a control level of signal.  
   
   
       17 . A composition comprising a labeled array information target that specifically binds to an array information probe.  
   
   
       18 . A kit comprising: 
 (a) an array information probe; and    (b) a target that binds to said array information probe under specific binding conditions to produce a signal and thereby provide information about an array.    
   
   
       19 . The kit of  claim 18 , further comprising instructions for using said array information probe and said target to provide information about a microarray.  
   
   
       20 . The kit of  claim 19 , wherein said probe is present in one or more array information elements on the surface on an array.  
   
   
       21 . The kit of  claim 18 , wherein said instructions include a protocol for spiking a sample with said target prior to contacting said array with said sample.  
   
   
       22 . A system for providing information about an array, said system comprising: 
 a) an array comprising one or more array information features; and    b) a target that specifically binds to at least one of said one or more array information features.    
   
   
       23 . A method of detecting the presence of an analyte in a sample, said method comprising: 
 (a) contacting a sample suspected of containing said analyte with an array of  claim 1 , wherein said array comprises a probe for said analyte;    (b) detecting any resultant binding complexes on the surface of said array to obtain binding complex data to determine whether said analyte is present in said sample.    
   
   
       24 . The method of  claim 23 , further comprising obtaining information about said array by assessing binding of target to said one or more array information features.  
   
   
       25 . The method of  claim 23 , wherein said analyte is a nucleic acid and said array is an array of nucleic acid probes.  
   
   
       26 . A method comprising transmitting a result obtained from a method of  claim 23  from a first location to a second location.  
   
   
       27 . The method of  claim 26 , wherein said second location is a remote location.  
   
   
       28 . A method comprising receiving a result of a method of  claim 23 .  
   
   
       29 . A hybridization assay comprising the steps of: 
 (a) contacting at least one sample containing nucleic acids labeled with a detectable label with a nucleic acid array comprising one or more array information features to produce a hybridization pattern for said nucleic acid sample; and    (b) analyzing said hybridization pattern for each detectable label to produce data on the amounts of said target nucleic acid in said sample and provide information about the array.    
   
   
       30 . A computer readable medium comprising programming to obtain information about an array from data obtained using the array.  
   
   
       31 . A computer-readable medium comprising: information for decoding encoded array information obtained from an array comprising one or more array information features.  
   
   
       32 . The computer readable medium of  claim 31 , wherein said array is an array of nucleic acids.  
   
   
       33 . The computer-readable medium of  claim 31 , wherein said information comprises a table that contains: a list of feature identifiers; and a list of probe identifiers corresponding to said feature identifiers.  
   
   
       34 . The computer-readable medium of  claim 33 , wherein said table indicates that certain features of said array are array information features.  
   
   
       35 . The computer readable medium of  claim 33 , wherein said table indicates which features correspond to which bit of a code.  
   
   
       36 . The computer-readable medium of  claim 31 , wherein said information indicates an executable program for decoding said encoded array information.  
   
   
       37 . The computer-readable medium of  claim 31 , wherein said information is a file that has a unique identifier that corresponds to a unique identifier of an array.  
   
   
       38 . The computer-readable medium of  claim 31 , wherein said array information features encode binary coded information, and said file contains information for decoding said binary coded information.  
   
   
       39 . A method for obtaining information about an array, comprising: reading an array comprising one or more array information features to provide encoded information for said array; and decoding said encoded information using a computer readable medium of  claim 31  to provide information about said array.  
   
   
       40 . The method of  claim 39 , wherein said array is a nucleic acid array.  
   
   
       41 . The method of  claim 39 , wherein said scanning provides a data file comprising feature identifiers and numerical assessments of the brightness of said array information features.  
   
   
       42 . The method of  claim 39 , wherein said decoding comprises identifying an executable program using said file, and executing said program, to decode said encoded information and provide information about said array.  
   
   
       43 . The method of  claim 42 , wherein said executable program is obtained from a remote location.  
   
   
       44 . A method for obtaining information about an array, comprising: encoding information on an array using one or more array information features; and providing information for decoding said encoded information.  
   
   
       45 . The method of  claim 44 , wherein said array information is provided from a location remote to said array.  
   
   
       46 . A method of assaying a sample, said method comprising: 
 (a) contacting said sample with an array comprising one or more array information features,    (b) reading said array with an array scanner to obtain data, and    (c) decoding said data using a computer readable medium of  claim 31  to provide information for said array.    
   
   
       47 . The method according to  claim 46 , wherein said array is a nucleic acid array.  
   
   
       48 . A method comprising transmitting a result obtained from a method of  claim 46  from a first location to a second location.  
   
   
       49 . The method of  claim 48 , where said second location is a remote location.  
   
   
       50 . A method comprising receiving data representing said data obtained by the method of  claim 46 .  
   
   
       51 . A kit for use with an array scanner, said kit comprising: 
 (a) a computer-readable medium according to  claim 31;  and    (b) instructions for operating said scanner according to said programming.    
   
   
       52 . The kit of  claim 51 , further comprising an array.  
   
   
       53 . A kit for use with an array scanner, said kit comprising: 
 (a) an array comprising array information features; and    (b) instructions for obtaining information for decoding encoded array information encoded by said array information features.    
   
   
       54 . A method, embodied in a computer program, for automated extraction data from a molecular array having features arranged in a regular pattern, the method comprising: 
 receiving a number of images of the molecular array, each produced by scanning the molecular array to determine intensities of data signals emanating from discrete positions on a surface of the molecular array;    estimating initial positions of selected marker features within an image of the molecular array;    calculating refined positions of the selected marker features within the image of the molecular array;    using the refined positions of the selected marker features to compute an initial coordinate system for locating features of the molecular array in the number of images of the molecular array;    using the initial coordinate system to locate positions of strong features within one or more images of the molecular array;    refining the positions of strong features within the one or more images of the molecular array by analyzing data signal intensity values in regions of the one or more images of the molecular array that contain the strong features;    using the refined positions of strong features in the one or more images of the molecular array to calculate a refined coordinate system to locate positions of weak features within the number of images of the molecular array;    using the refined positions of strong features in the one or more images of the molecular array to calculate a refined coordinate system to locate positions of local background regions surrounding all strong and weak features within the number of images of the molecular array; and    extracting data from strong features, and their respective local background regions, within the number of images of the molecular array using the refined positions of strong features within the number of images of the molecular array and extracting data from weak features, and their respective local background regions, within the number of images of the molecular array using locations for the weak features calculated from the refined coordinate system.    
   
   
       55 . The method of  claim 54  wherein data signals emanating from discrete positions on the surface of the molecular array include: 
 fluorescent emission from fluorophores incorporated into molecules bound to features of the molecular array;    radiation emitted by radioisotopes incorporated into molecules bound to features of the molecular array; and    light emission from chemoluminescent moieties incorporated into molecules bound to features of the molecular array.    
   
   
       56 . The method of  claim 54  wherein each image of the number of images comprise an array of pixels, each pixel having a data signal intensity value.  
   
   
       57 . The method of  claim 56  wherein the features of the molecular array are arranged in a rectilinear grid, wherein corner features are selected as marker features, and wherein estimating initial positions of selected marker features within an image of the molecular array further includes: 
 calculating row and column vectors by considering the values of pixels in rows and columns of the image;    determining a first and last peak in the row and column vectors; and    using pixel coordinates of the first and last peaks in the row vector to determine horizontal coordinates of the corner features and using pixel coordinates of the first and last peaks in the column vector to determine vertical coordinates of the corner features.    
   
   
       58 . A system for automated extraction of data from a molecular array having features arranged in a regular pattern, the system comprising: 
 a scanning component that produces images of the molecular array representing intensities of data signals emitted from discrete positions on a surface of the molecular array;    a computer program that processes the images of the molecular array produced by the scanning component to index features in the images of the molecular array corresponding to molecules bound to features of the molecular array and that extracts data from the indexed features within images of the molecular array; and a computer for executing the computer program.    
   
   
       59 . A The system of  claim 58  wherein data signal intensities emanating from discrete positions on the surface of the molecular array include: 
 radiation emitted by radioisotopes incorporated into molecules bound to features of the molecular array;    fluorescent emission from fluorophores incorporated into molecules bound to features of the molecular array; and    light emission from chemoluminescent moieties incorporated into molecules bound to features of the molecular array.    
   
   
       60 . The system of  claim 58  wherein the computer program processes the images of the molecular array and extracts data from indexed features within images of the molecular array by: 
 receiving a number of images of the molecular array produced by the scanning component;    estimating initial positions of selected marker features within an image of the molecular array;    calculating refined positions of the selected marker features within the image of the molecular array;    using the refined positions of the selected marker features to compute an initial coordinate system for locating features of the molecular array in the number of images of the molecular array;    using the initial coordinate system to locate positions of strong features within one or more images of the molecular array;    refining the positions of strong features within the one or more images of the molecular array by analyzing data signal intensity values in regions of the one or more images of the molecular array that contain the strong features;    using the refined positions of strong features in the one or more images of the molecular array to calculate a refined coordinate system to locate positions of weak features within the number of images of the molecular array;    using the refined positions of strong features in the one or more images of the molecular array to calculate a refined coordinate system to locate positions of local background regions surrounding all strong and weak features within the number of images of the molecular array; and    extracting data from strong features, and their respective local background regions, within the number of images of the molecular array using the refined positions of strong features within the number of images of the molecular array and extracting data from weak features, and their respective local background regions, within the number of images of the molecular array using locations for the weak features calculated from the refined coordinate system