System and method for creating magnified images of a microscope slide

Abstract

A method and system for creating a digital, virtual slide having optimum image quality characteristics. Multiple regions of a physical slide are identified as well as at least two focus z-positions z 1 , and z 2 . Each region of the physical slide is scanned (imaged) at the first z position, so as to produce a first set of digital images of each defined region. Each region of the physical slide is also scanned (imaged) at the second z position, so as to produce a second set of digital images of each defined region. Each image of each set is evaluated against a focus quality metric and, for each region, either the first or second image, corresponding to that region, is selected that exhibits a focus quality metric corresponding to a desired focus quality. These images are then merged into a digital virtual slide. Additional focus z-positions may be included, and the multiple z-positions may be scanned seriatim, sequentially, and/or in overlapping fashion.

1 . A method of creating a digital virtual microscope slide comprising:
 providing a microscopy system comprising a microscope, a digital imaging device, and a computer-controlled microscope stage;   providing a physical microscope slide;   defining multiple regions for the physical microscope slide;   defining a plurality of focus positions;   scanning each of the multiple regions at each of the plurality of focus positions using the microscopy system to produce a plurality of sets of digital images for each region, each set of digital images corresponding to a separate one of the focus positions;   evaluating each digital image of each set against a focus quality metric; and   selecting one digital image for each region from one of the pluraity of sets of digital images for that region, the selected digital image having a focus quality metric corresponding to a desired focus quality.   
     
     
         2 . The method of  claim 1 , wherein the regions are scanned by imaging each region at each of the plurality of focus positions before the next region is scanned. 
     
     
         3 . The method of  claim 1 , wherein the regions are scanned by imaging all of the regions, seriatim, at each of the focus positions. 
     
     
         4 . The method of  claim 1 , further comprising determining a nominal in-focus position for a sample slide adjusting the nominal in-focus position in a first direction by a first off-set, adjusting the nominal in-focus position in an opposite direction by a second off-set, and defining the first off-set and the second off-set as focus positions in the plurality of focus positions. 
     
     
         5 . The method of  claim 4 , further comprising determining the nominal in-focus position from a focus map. 
     
     
         6 . The method of  claim 4 , wherein the first off-set is unequal to the second off-set. 
     
     
         7 . The method of  claim 1 , wherein more than one of the regions is scanned simultaneously. 
     
     
         8 . The method of  claim 1 , wherein the microscopy system comprises a plurality of digital image devices arranged to capture multiple images of an optical field of view of the microscope, each of the digital image devices set at a separate one of the plurality of focus positions, and wherein the method further comprises simultaneously imaging a portion of the physical microscope slide presented to the optical field of view. 
     
     
         9 . The method of  claim 8 , wherein each of the plurality of digital imaging devices captures an image of the same portion of the physical microscope slide. 
     
     
         10 . The method of  claim 8 , wherein the digital imaging devices are disposed such that each of the plurality of digital imaging devices captures an image of separate portions of the physical slide. 
     
     
         11 . A microscopy system for creating a digital virtual microscope slide from a physical microscope slide, the system comprising:
 a microscope;   at least one digital imaging device,   a motorized microscope stage; and   a computer controllably coupled with the microscope, at least one digital imaging device, and motorized microscope stage, the computer programmed with an algorithm to:
 scan each of a plurality of regions of the physical microscope slide at a plurality of focus positions for each region, thereby producing a plurality of sets of digital images for each region, each set of digital images corresponding to a separate one of the focus positions; 
 evaluate each digital image of each set against a focus quality metric; and 
 select one digital image for each region from one of the plurality of sets of digital images for that region, the selected digital image having a focus quality metric corresponding to a desired focus quality. 
   
     
     
         12 . The system of  claim 11 , wherein the regions are scanned according to the algorithm by imaging each region at each of the plurality of focus positions before the next region is scanned. 
     
     
         13 . The system of  claim 11 , wherein the regions are scanned according to the algorithm by imaging all of the regions, seriatim, at each of the focus positions. 
     
     
         14 . The system of  claim 11 , wherein the algorithm further comprises determining a nominal in-focus position for a sample slide, adjusting the nominal in-focus position in a first direction by a first off-set, adjusting the nominal in-focus position in an opposite direction by a second off-set, and defining the first off-set and the second off-set as focus positions in the plurality of focus positions. 
     
     
         15 . The system of  claim 11 , wherein further comprising a plurality of digital image devices arranged to capture multiple images of an optical field of view of the microscope, each of the digital image devices set at a separate one of the plurality of focus positions, and wherein the algorithm further comprises simultaneously imaging a portion of the physical microscope slide presented to the optical field of view. 
     
     
         16 . The system of  claim 15 , wherein each of the plurality of digital imaging devices captures an image of the same portion of the physical microscope slide. 
     
     
         17 . The system of  claim 15 , wherein the digital imaging devices are disposed such that each of the plurality of digital imaging devices captures an image of separate portions of the physical slide. 
     
     
         18 . A method of creating a digital virtual microscope slide comprising:
 providing a microscopy system comprising a microscope and a digital imaging device;   providing a physical microscope slide;   defining multiple regions of the physical microscope slide;   scanning the physical microscope slide at a first focus position using the microscopy system to produce a first set of digital images of each defined region;   scanning the physical microscope slide at a second focus position using the microscopy system to produce a second set of digital images of each defined region;   evaluating each image of the first set of digital images and each image of the second set of digital images against a focus quality metric;   selecting one image having a focus quality metric corresponding to a desired focus quality for each region from either the firs set of digital images or the second set of digital images; and   merging the selected images into a composite image, the composite image defining the virtual slide.   
     
     
         19 . The method of  claim 18 , wherein the focus quality metric evaluation step is performed by measuring an image characteristic selected from the group consisting of overall image entropy, image texture energy, image contrast, and feature edge sharpness. 
     
     
         20 . A microscopy system for creating a digital virtual microscope slide from a physical microscope slide, the system comprising:
 a microscope;   at least one digital imaging device, and   a computer programmed with an algorithm to:
 define multiple regions for the physical microscope slide; 
 capture, for each defined region, a set of images, each image of the set characterized by a different focus position from other images of the set; 
 evaluating each image of each set against a focus quality metric; selecting, for each region, a particular one of the set of images corresponding to that region having a focus quality metric corresponding to a desired focus quality; 
 identifying the selected ones of each set of images as the chosen image of a corresponding region; and 
 merging the identified regional images into a composite image, the composite image defining the digital virtual microscope slide.