Reading chemical arrays

Abstract

Methods of using an addressable array of biopolymers which has been exposed to a sample, and apparatus and computer program products for use of the arrays. In one embodiment the method includes detecting signals from the exposed array to obtain a signal image of the array. The array signal image is saved in a memory. Based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image is established. A definition of the shapes of the established regions of each set is saved in a memory. Each region of each set is processed according to a corresponding routine for that set.

1 - 42 . (canceled)  
   
   
       43 . A method of reading an addressable array of biopolymers on a substrate, comprising: 
 (a) detecting signals from the exposed array to obtain a signal image of the array;    (b) establishing, based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image, wherein the shape of regions of a set include an identified shape of any of an array feature, a background region, and an identified inlier or outlier region within an array feature or background region; and    (c) processing each region of each set of a region processing routine.    
   
   
       44 . The method of  claim 43 , further comprising displaying the established shapes.  
   
   
       45 . The method of  claim 44 , wherein the displayed shapes are saved.  
   
   
       46 . The method of  claim 43 , wherein processed results from step (c) are saved.  
   
   
       47 . The method of  claim 44 , wherein the displayed shapes are saved in a first file and processed results from step (c) are saved in a second file.  
   
   
       48 . The method of  claim 43 , wherein the biopolymers comprise nucleic acids.  
   
   
       49 . The method of  claim 48 , wherein the biopolymers comprise DNA.  
   
   
       50 . The method of  claim 47 , wherein the first file is smaller than the second file.  
   
   
       51 . The method of  claim 47  additionally comprising, subsequent to processing of each region, retrieving the saved shapes of the established regions and displaying images of them.  
   
   
       52 . The method of  claim 43  additionally comprising, saving the array signal image, and subsequent to processing each region, retrieving the array signal image and saved shapes of the established regions and displaying overlaid images of them.  
   
   
       53 . The method of  claim 52 , wherein each displayed region is linked to processed results for that region.  
   
   
       54 . The method of  claim 53 , additionally comprising evaluating the results from the processing based on the displayed retrieved shapes.  
   
   
       55 . The method of  claim 54 , additionally comprising, based on the displayed retrieved shapes, altering a parameter used in the processing and re-processing a region using the altered parameter.  
   
   
       56 . The method of  claim 53  additionally comprising re-processing a region in response to an alteration of one of the shapes of a set using the altered shape.  
   
   
       57 . The method of  claim 52 , wherein the shape of regions of a first set are established which comprise regions of signal strength higher than a predetermined value representing detected array features, surrounded by regions of lower signal strength representing detected background.  
   
   
       58 . The method of  claim 57 , wherein the regions of the first set are processed by a first routine comprising a summation of signal strength within sub-regions of each first set region to provide a total signal strength for each first set region.  
   
   
       59 . The method of  claim 47 , wherein the shape of regions of a second set are established each of which comprises a local background region of lower signal strength than a corresponding detected feature about which the background region is positioned.  
   
   
       60 . The method of  claim 58 , wherein the first routine comprises subtracting local background region signal strength from the corresponding detected feature signal strength.  
   
   
       61 . An apparatus for reading an addressable array of biopolymers on a substrate which array has been exposed to a sample, comprising: 
 (a) a detector to detect signals from the exposed array to obtain a signal image of the array;    (b) a memory; and    (c) a processor which: establishes, based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image, wherein the shape of regions of a set include an identified shape of any of an array feature, a background region, and an identified inlier or outlier region within an array feature or background region; saves a definition of the shapes of the established regions of each set in a memory; and processes each region of each set of a region processing routine.    
   
   
       62 . The apparatus of  claim 61 , wherein the shapes of the established regions are saved in a first file and results of region processing are saved in a second file of the memory.  
   
   
       63 . The apparatus of  claim 61 , further comprising a display for displaying the established shapes.  
   
   
       64 . The apparatus of  claim 63 , wherein each displayed region is linked to processed results for that region.  
   
   
       65 . A computer program product, comprising: a computer readable storage medium having a computer program stored thereon for performing, when loaded into a computer, the steps of: 
 (a) receiving signals from a biopolymer array, as a signal image of the array;    (b) saving the array signal image in a memory;    (c) establishing, based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image, wherein the shape of regions of a set include an identified shape of any of an array feature, a background region, and an identified inlier or outlier region within an array feature or background region;    (d) saving a definition of the shapes of the established regions of each set in a memory; and    (e) processing each region of each set of a region processing routine.    
   
   
       66 . A method of reading an addressable array of biopolymers on a substrate which array has been exposed to a sample, comprising: 
 (a) detecting signals from the exposed array to obtain a signal image of the array;    (b) establishing, based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image, wherein the shape of regions of a set include an identified shape of an inlier or outlier region within an array feature; and    (c) processing each region of each set of a region processing routine.    
   
   
       67 . The method of  claim 66 , further comprising displaying the established shapes.  
   
   
       68 . The method of  claim 67 , further comprising saving the displayed shapes in a first file and the processed results in a second file.  
   
   
       69 . The method of  claim 66 , wherein the biopolymers comprise nucleic acids.  
   
   
       70 . The method of  claim 66 , wherein the biopolymers comprise DNA.  
   
   
       71 . The method of  claim 68  wherein the first file is smaller than the second file.  
   
   
       72 . The method of  claim 66  additionally comprising, subsequent to processing of each region, retrieving saved shapes of the established regions and displaying images of them.  
   
   
       73 . The method of  claim 66  additionally comprising, saving the array signal image, and subsequent to processing each region, retrieving the array signal image and saved shapes of the established regions and displaying overlaid images of them.  
   
   
       74 . The method of  claim 67  wherein each displayed region is linked to processed results for that region.  
   
   
       75 . The method of  claim 74 , additionally comprising evaluating the results from the processing based on the displayed retrieved shapes.  
   
   
       76 . The method of  claim 75  additionally comprising, based on the displayed retrieved shapes, altering a parameter used in the processing and re-processing a region using the altered parameter.  
   
   
       77 . The method of  claim 73  additionally comprising re-processing a region in response to an alteration of one of the shapes of a set using the altered shape.  
   
   
       78 . An apparatus for reading an addressable array of biopolymers on a substrate which array has been exposed to a sample, comprising: 
 (a) a detector to detect signals from the exposed array to obtain a signal image of the array;    (b) a memory; and    (c) a processor which: establishes, based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image, wherein the shape of regions of a set include an identified shape of an identified inlier or outlier region within an array feature; saves a definition of the shapes of the established regions of each set in a memory; and processes each region of each set of a region processing routine.    
   
   
       79 . The apparatus of  claim 78 , wherein the established shapes are saved in a first file and processed results are saved in a second file of the memory.  
   
   
       80 . The apparatus of  claim 78 , further comprising a display for displaying the established shapes.  
   
   
       81 . A computer program product, comprising: a computer readable storage medium having a computer program stored thereon for performing, when loaded into a computer, the steps of: 
 (a) receiving signals from a biopolymer array, as a signal image of the array;    (b) saving the array signal image in a memory;    (c) establishing, based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image, wherein the shape of regions of a set include an identified shape of an identified inlier or outlier region within an array feature;    (d) saving a definition of the shapes of the established regions of each set in a memory; and    (e) processing each region of each set of a region processing routine.