Methods for estimating probe cell locations in high-density synthetic DNA microarrays
First Claim
Patent Images
1. A method for estimating the probe cell locations in a hybridized microarray, comprising:
- obtaining an image of the intensity of a microarray having a plurality of individual probe cells;
estimating the center of individual probe cell locations in the image to provide the first estimated locations of the centers of estimated probe cell locations; and
for respective probe cell locations undergoing analysis;
generating a first fitting region that has a center that coincides with the location of the first estimated center and that has a boundary that can include partial pixel volumes;
obtaining pixel intensity data of the first fitting region;
generating a second fitting region that has a center that is spaced apart from the center of the first fitting region by less than about one pixel, the second fitting region having a boundary that can include partial pixel volumes;
obtaining pixel intensity data of the second fitting region;
comparing the variance of pixel intensity from the first and second fitting regions; and
determining the likely estimated probe cell location in the image based on the step of comparing the pixel intensity data in the first and second fitting regions.
1 Assignment
0 Petitions
Accused Products
Abstract
Methods, systems, and computer program products for estimating the location of a probe cell in an image of a high-density microarray DNA chip interrogate a plurality of different closely spaced estimated locations to identify the most likely estimated location of the probe cell in the image.
30 Citations
37 Claims
-
1. A method for estimating the probe cell locations in a hybridized microarray, comprising:
-
obtaining an image of the intensity of a microarray having a plurality of individual probe cells;
estimating the center of individual probe cell locations in the image to provide the first estimated locations of the centers of estimated probe cell locations; and
for respective probe cell locations undergoing analysis;
generating a first fitting region that has a center that coincides with the location of the first estimated center and that has a boundary that can include partial pixel volumes;
obtaining pixel intensity data of the first fitting region;
generating a second fitting region that has a center that is spaced apart from the center of the first fitting region by less than about one pixel, the second fitting region having a boundary that can include partial pixel volumes;
obtaining pixel intensity data of the second fitting region;
comparing the variance of pixel intensity from the first and second fitting regions; and
determining the likely estimated probe cell location in the image based on the step of comparing the pixel intensity data in the first and second fitting regions. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
-
-
20. A method for estimating the probe cell locations in an image of a hybridized high-density microarray having a plurality of individual hybridized probe cells thereon, comprising:
-
providing a first estimated center location of a respective probe cell location in the image;
generating an array of a plurality of potential estimated center locations such that the array includes the first estimated center as one of the estimated center locations;
interrogating a plurality of estimated probe cell locations, a respective one probe cell location having a center defined by one of the plurality of potential estimated center locations in the array to obtain pixel intensity data of pixels within the estimated probe cell locations; and
comparing the intensity data for each of the interrogated estimated probe cell locations to determine a likely estimated or revised estimated probe cell location. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27, 28)
-
-
29. A computer program product for estimating the probe cell locations of probe cells in an image of an expressed hybridized DNA microarray chip, the computer program product comprising:
-
a computer readable storage medium having computer readable program code embodied in said medium, said computer-readable program code comprising;
computer readable program code for obtaining an image of the intensities of a microarray having a plurality of individual probe cells;
computer readable program code for providing a first estimated center location of a respective probe cell location in the image;
computer readable program code for generating an array of a plurality of prospective estimated center locations for a respective probe cell such that the array includes the first estimated center as one of the estimated center locations;
computer readable program code for generating a fitting region for each of the plurality of plurality of prospective estimated center locations;
computer readable program code for interrogating the plurality of fitting regions to obtain pixel intensity data of pixels within estimated probe cell locations corresponding to the fitting regions; and
computer readable program code for comparing the intensity data for each of the interrogated estimated probe cell locations to determine a likely estimated or revised estimated probe cell location. - View Dependent Claims (30, 31, 32, 33, 34, 35, 36)
-
-
37. A system for estimating probe cell location in an image of a hybridized DNA array, comprising:
-
a processor; and
computer program code for estimating probe cell locations in an image of a hybridized microarray comprising, for a respective probe cell location in an image, interrogating a plurality of estimated probe cell locations by generating first and second fitting regions having centers which are spaced apart by less than about one pixel, the first and second fitting regions being able to include partial pixels at their boundaries, analyzing the pixel intensity variance within each of the first and second fitting regions, and selecting the potential estimated location for that probe cell based thereon.
-
Specification