Method, system, and computer code for finding spots defined in biological microarrays
First Claim
1. A method for processing data in digitized images of biological microarrays to identify one or more groupings of spots present in the microarray, the method comprising:
- importing a captured digitized image of a biological microarray of spots in an electronic format, the array comprising a plurality of approximately rectangular groupings of spots, called blocks, the groupings being defined by 1 through N, where N is an integer greater than 1, the blocks being arranged in a regular pattern, with rows and columns of blocks being separated by substantially horizontal and vertical isolation regions comprising background, the background regions being long, narrow areas approximating a rectangular shape, which are substantially free from any spots;
processing the captured image to reduce background noise from the captured image;
identifying at least the isolation region between the groupings in the captured image using a frequency domain filter applied to the captured image, the filter being constructed according to periodic components of the captured image, the periodic components being defined by a spatial distribution of the spots in the captured image of the microarray;
determining the locations of the boundaries of the groupings in the captured image of the biological microarray to isolate any one of the groupings from any one of the other groupings; and
storing the locations of the boundaries of the groupings in the captured image of the biological microarray into memory.
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Accused Products
Abstract
A method (and system) for using information contained within the scanned image to create, in an automated (or semi-automated) process, an accurate data grid. The process has steps: enhance the image; locate blocks of spots; and find each individual spot in each of the blocks. Preferably, the method makes use of image filtering using a “Principal Frequency Filter” based on a mathematical determination of major periodic elements in the image to eliminate noisy, non-periodic signals, and of smoothed intensity profiles of the filtered image data. Here, the term Principal Frequency Filter is used to indicate an image-enhancing filter based upon a mathematical operation which identifies the major periodic components of the image.
44 Citations
49 Claims
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1. A method for processing data in digitized images of biological microarrays to identify one or more groupings of spots present in the microarray, the method comprising:
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importing a captured digitized image of a biological microarray of spots in an electronic format, the array comprising a plurality of approximately rectangular groupings of spots, called blocks, the groupings being defined by 1 through N, where N is an integer greater than 1, the blocks being arranged in a regular pattern, with rows and columns of blocks being separated by substantially horizontal and vertical isolation regions comprising background, the background regions being long, narrow areas approximating a rectangular shape, which are substantially free from any spots; processing the captured image to reduce background noise from the captured image; identifying at least the isolation region between the groupings in the captured image using a frequency domain filter applied to the captured image, the filter being constructed according to periodic components of the captured image, the periodic components being defined by a spatial distribution of the spots in the captured image of the microarray; determining the locations of the boundaries of the groupings in the captured image of the biological microarray to isolate any one of the groupings from any one of the other groupings; and storing the locations of the boundaries of the groupings in the captured image of the biological microarray into memory. - View Dependent Claims (2, 3, 4, 5, 6)
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7. A method for processing data in a captured image of a biological microarray to identify the location of one or more spots defined in the microarray image, the method comprising:
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importing a captured digitized image of a biological microarray of spots in an electronic format, the array comprising a plurality of spots on a substrate material, the spots being defined by 1 through N, where N is an integer greater than 1, the spots being approximately equal in size and shape, the spots having been placed on the microarray in a predefined pattern which approximates a two dimensional lattice, each of the spots being identified by its row and column location in said lattice, each of the spots being provided on a background region, the spots generally distinguishable from the background region in the image by having higher values than the background in the case of a positive image or lower values than the background in the case of a negative image; enhancing the electronic image to improve the visibility of the spots against the background region; identifying the locations of the spots in the captured image by searching the enhanced electronic image for its local peak values; relating the identified location of each spot to its row and column location in the two dimensional grid by predicting each spot'"'"'s location from information about said grid and matching identified locations with predicted locations; and relating the one or more spots to respective one or more identifier information whereupon the identifier information uniquely identifies the spot. - View Dependent Claims (8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A system for processing data in captured digitized images of biological microarrays to identify the location of one or more spots defined in the microarray image, the system comprising one or more memories, the one or more memories including:
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a code directed to receiving a captured image of a biological microarray of spots in an electronic format, the array comprising a plurality of spots on a substrate material, the spots being defined by 1 through N, where N is an integer greater than 1, the spots being approximately equal in size and shape, the spots having been placed on the microarray in a predefined pattern which approximates a two dimensional lattice, each of the spots being identified by its row and column location in said lattice, each of the spots being provided on a background region, the spots generally distinguishable from the background region in the image by having higher values than the background in the case of a positive image or lower values than the background in the case of a negative image; a code directed to enhancing the electronic image to improve the visibility of the spots against the background region; a code directed to identifying the locations of the spots in the captured image by searching the enhanced electronic image for its local peak values; a code directed to relating the identified location of each spot to its row and column location in the two dimensional grid by predicting each spot'"'"'s location from information about said grid and matching identified locations with predicted locations; and a code directed to relating the one or more spots to respective one or more identifier information whereupon the identifier information uniquely identifies the spot. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25, 26)
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27. A method for processing data in biological microarrays to identify one or more spots defined in the microarray, the method comprising:
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importing a captured digitized image of a biological microarray of spots in an electronic format, the array comprising a plurality of spots on a substrate material, the spots being defined by 1 through N, where N is an integer greater than 1, the spots being approximately equal in size and shape, the spots having been placed on the microarray in a pattern which approximates a two dimensional grid, each of the spots being identified by its row and column location in said grid, each of the spots being provided on a background region, the background region including a covered region occupied by spots and an uncovered region being substantially free from any spots; mathematically defining a filter based on the principal frequency of the repeating spot grid; applying the filter to the captured image of the biological microarray to derive an enhanced image of the captured image, the filter being applied to enhance a spatial characteristic of the captured image; processing the enhanced image to identify spatial positions of the spots in the captured image; and relating the spatial positions of the spots to respective identifier information whereupon the identifier information uniquely identifies each of the spots. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38)
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39. A system for processing data in biological microarrays to identify one or more spots defined in the microarray, the system comprising one or more memories, the one or more memories including:
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a code directed to receiving an image of a biological microarray of spots in an electronic format, the array comprising a plurality of spots on a substrate material, the spots being defined by 1 through N, where N is an integer greater than 1, the spots having been placed on the substrate material in a pattern approximating a two dimensional grid, each of the spots being identified by its row and column location in said grid, each of the spots being provided on a background region, the background region including a covered region occupied by spots and an uncovered region being substantially free from any spots; a code directed to applying a filter to the captured image of the biological microarray to derive an enhanced image of the captured image, the filter being applied to enhance a spatial characteristic of the captured image; a code directed to identifying the locations of the spots by searching the enhanced electronic image for its highest values; a code directed to constructing a predicted spot location grid from frequency and phase information from the enhanced spatial characteristics of the captured image; and a code directed to processing the enhanced image to identify spatial positions of the spots in the captured image. - View Dependent Claims (40, 41, 42, 43, 44, 45, 46, 47)
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48. A method for processing data in biological microarrays to identify one or more spots defined in the microarray, the method comprising:
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providing an image of a biological microarray of spots in an electronic format, the image being a captured image, the array comprising a plurality of spots on a substrate material, the spots being defined by 1 through N, where N is an integer greater than 1, the spots having been placed on the microarray in a pattern approximating a two dimensional grid, each of the spots being identified by its row and column location in said grid, each of the spots being provided on a background region, the background region including a covered region occupied by spots and an uncovered region being substantially free from any spots; processing a two dimensional representation associated with the captured image of the biological microarray using a processing filter to provide an enhanced image of the captured image, the filter being derived from a two dimensional power spectrum of the two dimensional representation associated with the captured image by selecting two of the strongest non-zero frequency components and removing other frequency components outside of a frequency domain region associated with the two of the strongest non-zero frequency components; processing the enhanced image to identify spatial positions of the spots in the captured image; and relating the spatial positions of the spots to respective identifier information whereupon the identifier information uniquely identifies each of the spots. - View Dependent Claims (49)
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Specification