Method and apparatus for screening chemical compounds

Abstract

Methods and apparatus for screening large numbers of chemical compounds and performing a wide variety of fluorescent assays, including live cell assays. The methods utilize a laser linescan confocal microscope with high speed, high resolution and multi-wavelength capabilities and real time data-processing. Imaging may be done at video-rates and with use of ultraviolet illumination.

What is claimed is:  
     
         1 . A method for processing biological sample image data, comprising: 
 acquiring a digital image of a biological sample using a imaging system, wherein the digital image includes a target object and a background, wherein the digital image has a plurality of digital image pixels, and wherein each digital image pixel has a digital image intensity value represented by a plurality of bits;    converting the digital image to a bitmap, wherein the bitmap has a plurality of bitmap pixels, wherein each bitmap pixel has a bitmap intensity value represented by a single bit, and wherein the digital image pixels and bitmap pixels have coordinates;    performing bitmap operations on the bitmap to isolate the target object from the background and to thereby identify those bitmap pixels having a set of related coordinates belonging to the target object; and    using the set of related coordinates to perform calculations on the digital image pixels having those coordinates.    
     
     
         2 . The method defined in  claim 1  further comprising identifying a bounding box that encloses the target object.  
     
     
         3 . The method defined in  claim 1  further comprising counting those bitmap pixels that have the set of related coordinates belonging to the target object.  
     
     
         4 . The method defined in  claim 1 , wherein the target object has a boundary, the method further comprising using an erosion process to exclude some of the bitmap pixels that have the set of related coordinates belonging to the target object from the boundary of the target object.  
     
     
         5 . The method defined in  claim 1 , wherein the target object has a boundary, the method further comprising using a dilation process to advance the boundary of the target object outward into the background.  
     
     
         6 . The method defined in  claim 1  further comprising processing the bitmap pixels having the set of related coordinates belonging to the target object to study target object shape.  
     
     
         7 . The method defined in  claim 1  further comprising processing the bitmap pixels having the set of related coordinates belonging to the target object to study target object orientation.  
     
     
         8 . The method defined in  claim 1  wherein acquiring the digital image comprises acquiring digital image data corresponding to the emission of at least two fluorescent labels.  
     
     
         9 . The method defined in  claim 1  wherein acquiring the digital image comprises acquiring digital image data corresponding to the emission of at least two fluorescent labels, the method further comprising using a co-localization analysis routine to determine how much of a first fluorescently-labeled species is localized with respect to a second fluorescently-labeled species in the biological sample.  
     
     
         10 . The method defined in  claim 1  wherein acquiring the digital image comprises acquiring digital image data corresponding to the emission of at least two fluorescent labels, the method further comprising using a co-localization analysis routine to determine in real time how much of a first fluorescently-labeled species is localized with respect to a second fluorescently-labeled species in the biological sample.  
     
     
         11 . The method defined in  claim 1  wherein acquiring the digital image comprises acquiring digital image data corresponding to the emission of at least two fluorescent labels, the method further comprising using a translocation data analysis routine to determine how much a first fluorescently-labeled species is distributed in a correlated or anti-correlated manner with respect to a second fluorescently-labeled species in the biological sample.  
     
     
         12 . The method defined in  claim 1  further comprising tracking individual cells in the biological sample.