Automated Detection of Cell Colonies and Coverslip Detection Using Hough Transforms
First Claim
1. A method for an automatic detection of cell colonies, comprising:
- acquiring digital images of sub-areas of a slide;
generating background intensity images;
forming background-subtracted sub-area images by subtracting the minimum of a morphologically processed image and the original digital image from the original image;
generating shrunk sub-area images by shrinking the background-subtracted sub-area images by a predefined scale factor;
stitching the shrunk sub-area images into a composite image representing the entire slide;
converting the composite image into a binary edge image by the application of an automatic thresholding technique;
passing the binary edge image through a Hough transform to produce a Hough space transformed image;
analyzing the Hough space transformed image to identify peaks representing a coverslip edge location;
subjecting the Hough space transformed image to an inverse Hough transform to convert said peaks back to the edges of the coverslip in the binary edge image;
setting to zero all pixels of the composite image outside of the coverslip area;
morphologically processing the composite binary edge image;
identifying colonies in the composite binary edge image;
eliminating unwanted colonies from the composite binary edge image based on their size or morphology;
recording the location, size, or binary image masks of the remaining colonies on the slide;
generating a map of automatic focusing values over the remaining colonies on the slide using a high power objective;
acquiring a plurality of high power images over the remaining colonies on the slide using a high power objective and the map of automatic focusing values;
performing metaphase detection; and
assigning each detected metaphase to a colony.
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Abstract
The present invention provides methods and systems for automatic detection of the location of cell colonies on a specimen slide, in particular under the coverslip of a specimen slide. Slide scanning can be performed using an automated microscope with motorized axes. The location of the colonies can be determined by image analysis, which is followed by automatically finding metaphase cells and associating them with each colony. The invention also provides an automated, Hough-transform-based method for identifying the location of the slide coverslip and, if desired, analyzing only the image area contained within the coverslip.
21 Citations
58 Claims
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1. A method for an automatic detection of cell colonies, comprising:
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acquiring digital images of sub-areas of a slide; generating background intensity images; forming background-subtracted sub-area images by subtracting the minimum of a morphologically processed image and the original digital image from the original image; generating shrunk sub-area images by shrinking the background-subtracted sub-area images by a predefined scale factor; stitching the shrunk sub-area images into a composite image representing the entire slide; converting the composite image into a binary edge image by the application of an automatic thresholding technique; passing the binary edge image through a Hough transform to produce a Hough space transformed image; analyzing the Hough space transformed image to identify peaks representing a coverslip edge location; subjecting the Hough space transformed image to an inverse Hough transform to convert said peaks back to the edges of the coverslip in the binary edge image; setting to zero all pixels of the composite image outside of the coverslip area; morphologically processing the composite binary edge image; identifying colonies in the composite binary edge image; eliminating unwanted colonies from the composite binary edge image based on their size or morphology; recording the location, size, or binary image masks of the remaining colonies on the slide; generating a map of automatic focusing values over the remaining colonies on the slide using a high power objective; acquiring a plurality of high power images over the remaining colonies on the slide using a high power objective and the map of automatic focusing values; performing metaphase detection; and assigning each detected metaphase to a colony. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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16. An apparatus for an automatic detection of cell colonies, comprising:
- an optical system comprising a digital camera for acquiring digital images of the slide, a computing unit for storing and processing the digital images of the slide, said computing unit executing a method so as to cause;
images of sub-areas of a slide to be acquired by digital camera with a low power objective at a fixed calibrated focus; background intensity images to be generated; a background-subtracted sub-area images to be formed by subtracting the minimum of a morphologically processed image and the original digital image from the original image; shrunk sub-area images to be generated by shrinking the background-subtracted sub-area images by a predefined scale factor; the shrunk sub-area images to be stitched into a composite image representing the entire slide; the composite image to be converted into a binary edge image by the application of an automatic thresholding technique; the binary edge image to be passed through a Hough transform to produce a Hough space transformed image; the Hough space transformed image to be analyzed to identify peaks, representing coverslip edge location; the Hough space transformed image to be subjected to the inverse Hough transform to convert said peaks back to the edges of the coverslip in the binary edge image; all pixels of the composite image to be set to zero outside of the coverslip area; the composite binary edge image to be morphologically processed; colonies in the composite binary edge image to be identified; unwanted colonies from the composite binary edge image to be eliminated based on their size or morphology; the location, size, or binary image masks of the remaining colonies on the slide to be recorded; a map of automatic focusing values over the remaining colonies on the slide to be generated using a high power objective; a plurality of high power images to be acquired over the remaining colonies on the slide using a high power objective and the map of automatic focusing values; metaphase detection to be performed; and each detected metaphase to be assigned to a colony. - View Dependent Claims (17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
- an optical system comprising a digital camera for acquiring digital images of the slide, a computing unit for storing and processing the digital images of the slide, said computing unit executing a method so as to cause;
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29. A method for an automatic detection of slide coverslips, comprising:
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acquiring digital images of sub-areas of the slide; generating background intensity images; forming background-subtracted sub-area images by subtracting the minimum of a morphologically processed image and the original digital image from the original image; generating shrunk sub-area images by shrinking the background-subtracted sub-area images by a predefined scale factor; stitching the shrunk sub-area images into a composite image representing the entire slide; converting the composite image into a binary edge image by the application of an automatic thresholding technique; passing the binary edge image through a Hough transform to produce a Hough space transformed image; analyzing the Hough space transformed image to identify peaks representing a coverslip edge location; subjecting the Hough space transformed image to an inverse Hough transform to convert said peaks back to the edges of the coverslip in the binary edge image; and setting to zero all pixels of the composite image outside of the coverslip area. - View Dependent Claims (30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44)
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45. An apparatus for an automatic detection of slide coverslips, comprising:
- an optical system comprising a digital camera for acquiring digital images of the slide, a computing unit for storing and processing the digital images of the slide, said computing unit executing a method so as to cause;
images of sub-areas of a slide to be acquired by digital camera with a low power objective at a fixed calibrated focus; background intensity images to be generated; a background-subtracted sub-area images to be formed by subtracting the minimum of a morphologically processed image and the original digital image from the original image; shrunk sub-area images to be generated by shrinking the background-subtracted sub-area images by a predefined scale factor; the shrunk sub-area images to be stitched into a composite image representing the entire slide; the composite image to be converted into a binary edge image by the application of an automatic thresholding technique; the binary edge image to be passed through a Hough transform to produce a Hough space transformed image; the Hough space transformed image to be analyzed to identify peaks, representing coverslip edge location; the Hough space transformed image to be subjected to the inverse Hough transform to convert said peaks back to the edges of the coverslip in the binary edge image; and all pixels of the composite image to be set to zero outside of the coverslip area. - View Dependent Claims (46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58)
- an optical system comprising a digital camera for acquiring digital images of the slide, a computing unit for storing and processing the digital images of the slide, said computing unit executing a method so as to cause;
Specification