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 - 10 . (canceled)  
     
     
         11 . An apparatus comprising: 
 a light source;    an optical train for directing light from said light source at a substrate including a surface having fluorescently marked regions;    a translation system co-operatively arranged with said optical train and constructed to support and displace said substrate;    an auto-focusing system constructed and arranged to focus said directed light onto said surface;    a detector for detecting fluorescent light from said fluorescently marked regions of said surface in response to said light; and    a computer arranged to control operation of said light source, said detector, said translation system and said auto-focusing system to execute auto-focusing by controlling said translation system and bringing into focus corners of said surface; said computer being further arranged to receive data from said detector corresponding to said detected fluorescent light and provide a data file representing an array of photon counts as a function of a pixel position on said surface.    
     
     
         12 . The apparatus of  claim 11 , wherein said computer is further arranged to generate an image file including data indicative of fluorescence intensity level as a function of said substrate pixel position.  
     
     
         13 . The apparatus of  claim 11 , wherein said detector comprises a confocal detector including a pinhole.  
     
     
         14 . The apparatus of  claim 11 , wherein said detector comprises a photodiode utilized for said auto-focusing and a photomultiplier for detecting said fluorescent light.  
     
     
         15 . The apparatus of  claim 11 , wherein said computer executes said auto-focusing by interpolating focusing values determined for said corners of said surface having a planar shape.  
     
     
         16 . The apparatus of  claim 11 , wherein said computer executes said auto-focusing by bringing into focus all four of said corners of said surface.  
     
     
         17 . The apparatus of  claim 16 , wherein said computer executes said auto-focusing by interpolating focusing values determined for said four corners of said surface having a planar shape.  
     
     
         18 . The apparatus of  claim 11 , wherein said translation system includes an x-y-z-translation stage.  
     
     
         19 . The apparatus of  claim 11 , wherein said optical train separates reflected excitation light from said surface of said substrate from fluoresced light from said surface.  
     
     
         20 . An apparatus comprising: 
 a light source constructed to emit excitation light;    an optical train for directing said excitation light from said light source at a substrate including a surface having fluorescently marked regions;    a translation system co-operatively arranged with said optical train and constructed to support and displace said substrate;    an auto-focusing system constructed and arranged to focus said excitation light onto said surface;    a detector for detecting fluorescent light from said fluorescently marked regions of said surface in response to said excitation light; and    a computer arranged to receive data from said detector corresponding to said detected fluorescent light of individual pixels of said surface and determine a dynamic range for data scaling; said computer being further arranged to scale said data and provide a data file representing an array of photon counts as a function of a pixel position on said surface.    
     
     
         21 . The apparatus of  claim 20 , wherein said computer is further arranged to scale said data using logarithmic scaling.  
     
     
         22 . The apparatus of  claim 21 , wherein said computer is further arranged to generate an image file including data indicative of fluorescence intensity level as a function of said substrate pixel position.  
     
     
         23 . The apparatus of  claim 20 , wherein said computer is further arranged to scale said data using linear scaling.  
     
     
         24 . The apparatus of  claim 23 , wherein said computer is further arranged to generate an image file including data indicative of fluorescence intensity level as a function of said substrate pixel position.  
     
     
         25 . The apparatus of  claim 24 , wherein said computer is arranged to control operation of said light source, said detector, said translation system and said auto-focusing system to execute auto-focusing by controlling said translation system and bringing into focus corners of said surface  
     
     
         26 . The apparatus of  claim 25 , wherein said auto-focusing system determines a focal plane of the light passing through said optical train.  
     
     
         27 . The apparatus of  claim 26 , wherein said optical train separates reflected excitation light from said surface of the substrate from fluoresced light from said surface.