US 6,349,144 B1 · Automated DNA array segmentation and analysis

Abstract

A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. The frame is stored in a memory device and a set of image information within said frame including a selected set of the DNA spot images is selected. A grid including a plurality of spaced grid points corresponding to said selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame. The current position of one or more grid points are adjusted by: selecting a first bounding area in the frame around the current position of the grid point; generating a first position update including position information for updating a current position of said grid point to a first new position within the first bounding area, the location of said first new position relative to said current position being a function of intensity level of at least a portion of the image within the first bounding area; generating a second position update including position information for updating said current position to a second new position in the frame, said second new position being in a geometric arrangement with the position of grid points around said grid point; and updating said current position with the position information of the first and the second position updates, thereby shifting said grid point toward the corresponding spot image. A display method diaplays image information corresponding to a plurality of DNA spot images of at least one DNA spot, the image information including image characteristic values including background and signal intensity levels. For each DNA spot image: (1) background and signal intensity levels are extracted from the image characteristic values for the spot image, and (2) difference values between the background intensity levels and signal intensity levels are determined. For each DNA spot: (1) the corresponding difference values are related a range of graphic values, (2) a graphic value for each difference value is selected; and (3) the selected graphic values are displayed.

Claims94

Dependent claims

A method for segmentation of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots, said image information including image intensity level information corresponding to said DNA spots, the method comprising the steps of:

(a) storing the frame of image information in a memory device;
(b) selecting a set of image information within said frame including a selected set of the DNA spot images;
(c) generating a grid in said memory device, the grid including a plurality of spaced grid points corresponding to said selected DNA spot images, each grid point including position information indicating the position of the grid point within said frame;
and
(d) modifying a current position of at least one grid point corresponding to a spot image in said selected image, including the steps of:
(i) selecting a first bounding area in the frame around the current position of the grid point;
(ii) generating a first position update including position information for updating a current position of said grid point to a first new position within the first bounding area, the location of said first new position relative to said current position being a function of intensity level of at least a portion of the image within the first bounding area;
(iii) generating a second position update including position information for updating said current position to a second new position in the frame, said second new position being in a geometric arrangement with the position of one or more grid points around said grid point;
and
(iv) updating said current position with the position information of the first and the second position updates, thereby shifting said grid point toward the corresponding spot image.

7 more elements

A software system for configuring a computer system comprising a processor, and a memory device, for segmentation of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots, said image information including image intensity level and intra frame position information corresponding to said DNA spots, the software system comprising program instructions for:

(a) storing the frame of image information in the memory device;
(b) selecting a set of image information within said frame including a selected set of the DNA spot images;
(c) generating a grid in said memory device, the grid including a plurality of spaced grid points corresponding to said selected DNA spot images, each grid point including position information indicating the position of the grid point within said frame;
and
(d) modifying a current position of at least one grid point corresponding to a spot image in said selected image, including the steps of:
(i) selecting a first bounding area in the frame around the current position of the grid point;
(ii) generating a first position update including position information for updating a current position of said grid point to a first new position within the first bounding area, the location of said first new position relative to said current position being a function of intensity level of at least a portion of the image within the first bounding area;
(iii) generating a second position update including position information for updating said current position to a second new position in the frame, said second new position being in a geometric arrangement with the position of one or more grid points around said gird point;
and
(iv) updating said current position with the position information of the first and the second position updates, thereby shifting said grid point toward the corresponding spot image.

7 more elements

A computer system for segmentation of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots, said image information including image intensity level and intra frame position information corresponding to said DNA spots, the computer system comprising:

(b) means for selecting a set of image information within said frame including a selected set of the DNA spot images;
(c) means for generating a grid in a memory device, the grid including a plurality of spaced grid points corresponding to said selected DNA spot images, each grid point including position information indicating the position of the grid point within said frame;
and
(d) means for modifying a current position of at least one grid point corresponding to a spot image in said selected image, including:
(i) means for selecting a first bounding area in the frame around the current position of the grid point;
(ii) means for generating a first position update including position information for updating a current position of said grid point to a first new position within the first bounding area, the location of said first new position relative to said current position being a function of intensity level of at least a portion of the image within the first bounding area;
(iii) means for generating a second position update including position information for updating said current position to a second new position in the frame, said second new position being in a geometric arrangement with the position of one or more grid points around sais grid point;
and
(iv) means for updating said current position with the position information of the first and the second position updates, thereby shifting said grid point toward the corresponding spot image.

6 more elements

(a) storing the frame of image information in memory;
(b) selecting a set of image information within said frame including a selected set of the DNA spot images;
(c) generating a grid in memory, the grid including a plurality of spaced grid points corresponding to said selected set of DNA spot images, the grid points having a predefined relationship, each grid point including position information indicating the position of the grid point within said image frame, wherein the current position of one or more of the grid points can be modified in relation to other grid points;
(d) modifying a current position of at least one grid point corresponding to a spot image in said selected image, by modifying the position information of said grid point, based on properties of one or more spot images to shift said grid point toward the corresponding spot image;
and
(e) segmenting the selected set of image information by selecting at least one image segment defining a segment area around a grid point and including a spot image.

3 more elements

A software system for configuring a computer system comprising a processor, and memory, for segmentation of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots, said image information including image intensity level and intra frame position information corresponding to said DNA spots, the software system comprising program instructions for:

(a) storing the frame of image information in memory;
(b) selecting a set of image information within said frame including a selected set of the DNA spot images;
(c) generating a grid in memory, the grid including a plurality of spaced grid points corresponding to said selected set of DNA spot images, the grid points having a predefined relationship, each grid point including position information indicating the position of the grid point within said image frame, wherein the current position of one or more of the grid points can be modified in relation to other grid points;
(d) modifying a current position of at least one grid point corresponding to a spot image in said selected image, by modifying the position information of said grid point, based on properties of one or more spot images to shift said grid point toward the corresponding spot image;
and
(e) segmenting the selected set of image information by selecting at least one image segment defining a segment area around a grid point and including a spot image.

3 more elements

Dependencies are inferred from the claim text.

Automated DNA array segmentation and analysis

Life of this patent

Automated DNA array segmentation and analysis

Life of this patent

Abstract

Claims94