Method and apparatus for detection of fluorescently labeled materials

Abstract

Fluorescently marked targets bind to a substrate 230 synthesized with polymer sequences at known locations. The targets are detected by exposing selected regions of the substrate 230 to light from a light source 100 and detecting the photons from the light fluoresced therefrom, and repeating the steps of exposure and detection until the substrate 230 is completely examined. The resulting data can be used to determine binding affinity of the targets to specific polymer sequences.

1 . A method for evaluating an orientation of a molecular array having features arranged in a pattern, comprising: 
 (a) receiving an image of the molecular array produced by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array;    (b) calculating an actual result of a function on pixels of the image along an axis of the image;    (c) comparing the result of step (b) with an expected result that would be obtained if the features were arranged in a pattern having a predetermined orientation.    
   
   
       2 . The method of  claim 1 , wherein the intensity values of pixels along the axis are summed to form a vector.  
   
   
       3 . The method of  claim 2 , wherein intensity values are summed along a horizontal axis of the image to form a row vector.  
   
   
       4 . The method of  claim 2 , wherein intensity values are summed along a vertical axis of the image to form a column vector.  
   
   
       5 . The method of  claim 2 , wherein intensity values are summed along a horizontal axis of the image to form a row vector and along a vertical axis of the image to form a column vector.  
   
   
       6 . The method of  claim 2 , further comprising using the positions of first and last peaks in the vector to estimate the positions of the corner features within the image.  
   
   
       7 . The method of  claim 1 , wherein the features are arranged in a rectilinear grid of rows and columns.  
   
   
       8 . The method of  claim 1 , wherein the result of step (b) is compared with different expected results based on different predetermined orientations until a match is obtained.  
   
   
       9 . The method of  claim 1 , wherein: when the results of the comparison in step (c) are outside a predetermined difference, then altering the orientation of the pattern of features having the predetermined orientation and repeating steps (b) and (c).  
   
   
       10 . The method of  claim 9 , wherein the orientation is rotated.  
   
   
       11 . The method of  claim 9 , wherein steps (b) and (c) are repeated until the results of the comparison are within the predetermined distance.  
   
   
       12 . The method of  claim 1 , additionally comprising: obtaining information on the array's layout using a code associated with the array, and evaluating the pattern of pixels based on the obtained information.  
   
   
       13 . The method of  claim 12 , wherein the array's layout is obtained from a remote location.  
   
   
       14 . The method of  claim 1 , further comprising subdividing the array of features into regions, and summing intensity values of pixels along an axis of an image of the region.