Scanning parameterization for biopolymeric array scanner

Abstract

Methods for programming an array scanner to scan a plurality of biopolymer arrays are provided. In the subject methods, individual scanning parameters for at least two different arrays of the plurality of arrays to be scanned are selected and input into the array scanner prior to scanning the plurality arrays. The programmed scanner then scans the plurality of arrays according to the pre-selected scanning parameters Also provided are scanners programmed according to the subject methods, as well as computer programming that provides for programming of scanners according to the subject methods. The subject methods and compositions find use in a variety of different applications, including both genomics and proteomics applications.

1 . A method of programming a biopolymer array scanner to scan a plurality of biopolymeric arrays, said method comprising: 
 individually selecting different scanning parameters for at least two different biopolymeric arrays of said plurality prior to using said scanner to scan said plurality of arrays, wherein said scanning parameters include at least one scanning parameter selected to modulate the way a scanner scans a particular array.    
   
   
       2 . The method according to  claim 1 , wherein said method further includes selecting a scan region.  
   
   
       3 . The method according to  claim 1 , wherein said scanning parameter is a detector sensitivity setting for a first channel.  
   
   
       4 . The method according to  claim 3 , wherein said scanning parameter is a photomultiplier tube setting for said first channel.  
   
   
       5 . The method according to  claim 1 , wherein said scanning parameter is a detector sensitivity setting for a second channel.  
   
   
       6 . The method according to  claim 5 , wherein said scanning parameter is a photomultiplier tube setting for said second channel.  
   
   
       7 . The method according to  claim 1 , wherein said scanning parameter is a dye channel.  
   
   
       8 . The method according to  claim 1 , wherein said scanning parameter is an output file path.  
   
   
       9 . The method according to  claim 1 , wherein said scanner comprises a barcode reader and a barcode on a surface of an array substrate allows automatic selection of the scanning parameters associated with said barcode by said scanner.  
   
   
       10 . The method according to  claim 1 , wherein said scanning parameters are set through retrieval of said parameters from a database via scanning of barcodes on the a surface of said at least two different biopolymeric arrays.  
   
   
       11 . The method according to  claim 1 , wherein said at least one of said individually selected scanning parameters is a default parameter.  
   
   
       12 . The method according to  claim 1 , wherein the biopolymeric array is an array of polynucleotides or polypeptides.  
   
   
       13 . A computer-readable medium comprising program that allows an array scanner to be programmed according to the method of  claim 1 .  
   
   
       14 . The computer readable medium according to  claim 13 , wherein said program provides a user interface which presents to a user the option of individually selecting at least one scanning parameter for two or more of a plurality of slides.  
   
   
       15 . A biopolymer array scanner comprising a computer-readable medium according to  claim 13 .  
   
   
       16 . (canceled)  
   
   
       17 . A method of scanning a plurality of biopolymeric arrays, said method comprising: 
 (a) programming a biopolymer array scanner according to the method of  claim 1;  and    (b) scanning said plurality of biopolymeric arrays using said programmed scanner.    
   
   
       18 . The method of  claim 17 , wherein the biopolymeric array is an array of polynucleotides or polypeptides.  
   
   
       19 - 22 . (canceled)  
   
   
       23 . The method of  claim 1 , wherein said method further comprises generating an output file associated with an individual array and associating data with the output file.  
   
   
       24 . The method of  claim 23 , wherein the data associated with the output file is selected from the group consisting of: an array description, the identity of a scanner operator, an error handling option, post processing options, a script for an email, and combinations thereof.