Data processing system and methods

Patent metadata

Field	Value
Publication number	US-8965076-B2
Application number	US-201113006206-A
Country	US
Kind code	B2
Filing date	Jan 13, 2011
Priority date	Jan 13, 2010
Publication date	Feb 24, 2015
Grant date	Feb 24, 2015

Abstract

Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

First claim

What is claimed is:

1. A method of tracking the location of features of a specimen across a set of images of the specimen captured at different reference points, wherein said specimen comprises at least one tile comprising an array of molecules, wherein said array of molecules comprises a plurality of features, wherein a feature of said plurality of features comprises multiple copies of a molecule of said array of molecules, wherein said molecule comprises a nucleic acid, said method comprising the steps of:
(a) providing a labeled nucleotide base to said array of molecules, thereby extending a primer hybridized to a nucleic acid within a feature so as to produce a signal corresponding to a feature comprising said nucleic acid,
wherein each image in said set of images includes colors signals,
wherein a different color corresponds to a different nucleotide base,
wherein each image of the set of images comprises signals having a single color selected from four different colors,
wherein four different labeled nucleotide bases are provided to said array of molecules so as to produce four different images, each image comprising signals having a single color,
wherein the signal color is different for each of the four different images, thereby producing a cycle of four color images that corresponds to the four possible nucleotides present at a particular position in said nucleic acid;

(b) providing additional labeled nucleotide bases to said array of molecules, thereby producing a plurality of cycles of color images;
(c) selecting a subset of images, wherein the images of the subset depict signals corresponding to features of the specimen, and wherein the images of the subset are captured at different reference points;
(d) selecting a primary image comprising either a single image or a compilation of multiple merged images from the subset of images, said selecting comprising:
(d1) selecting the four different color images from a single cycle within the subset of images,
(d2) merging signals from at least two different color images of each cycle into a candidate primary image for said cycle,
(d3) repeating steps (d1) and (d2), thereby forming a plurality of candidate primary images, and
(d4) selecting the candidate primary image from among the candidate primary images that includes the most signals, thereby obtaining a primary image;

(e) registering the signals depicted in the images of the subset of images with the signals depicted in the primary image, so as to determine the location of the signals depicted in the images with respect to each other, thereby producing signal clumps;
(f) selecting a signal from each of said signal clumps, thereby forming a template that permits the identification of the locations of features of said specimen; and
(g) registering remaining images in said set of images with said template.

2. The method of claim 1 further comprising the step of selecting a secondary image, wherein said secondary image is the candidate primary image that includes the second most signals.

3. The method of claim 2 , wherein said secondary image comprises either a single image or a compilation of multiple merged images.

4. The method of claim 3 further comprising registering the signals from the secondary image with the signals from the primary image.

5. The method of claim 4 further comprising registering signals from nonselected images with the signals from the secondary image, wherein said nonselected images are obtained from the image cycle from which the primary image was obtained.

6. The method of claim 5 further comprising registering signals from remaining images in the subset with signals from the primary image.

7. The method of claim 1 , wherein the signals from at least two different color images are subject to cross-talk, and wherein cross-talk between two signal channels allows signals from one color image to appear in the other color image.

8. The method of claim 1 , wherein the signals from at least two different color images comprise signals corresponding to A and C.

9. The method of claim 1 , wherein said template that permits the identification of the locations of features of said specimen is saved to a locations file.

10. A method of generating a template for image registration, said method comprising the steps of:
(a) selecting a subset from a set of images of a specimen, said subset of images comprising a plurality of image cycles, wherein the images of the subset depict signals corresponding to features of the specimen, and wherein the images of the subset are captured at different reference points;
(b) selecting a primary image from the subset of images, wherein said primary image is the image having the most signals from the subset of images;
(c) selecting a secondary image from the subset of images, wherein said secondary images is the image having the second most signals from the subset of images; and
(d) registering the signals from the secondary image with the signals from the primary image;
(e) registering signals from nonselected images with the signals from the secondary image, wherein said nonselected images are obtained from the image cycle from which the primary image was obtained;
(f) registering signals from remaining images in the subset with signals from the primary image, so as to determine the location of the signals depicted in the images with respect to each other, thereby producing signal clumps; and
(g) selecting a signal from each of said signal clumps, thereby forming a template that permits the identification of the locations of features of said specimen.

11. A system for generating a template for image registration, said system comprising:
a processor;
a storage capacity; and
a program for generating a template for image registration, said program comprising instructions for:
(a) selecting a subset from a set of images of a specimen, said subset of images comprising a plurality of image cycles, wherein the images of the subset depict signals corresponding to features of the specimen, and wherein the images of the subset are captured at different reference points;
(b) selecting a primary image from the subset of images, wherein said primary image is the image having the most signals from the subset of images;
(c) selecting a secondary image from the subset of images, wherein said secondary images is the image having the second most signals from the subset of images; and
(d) registering the signals from the secondary image with the signals from the primary image;
(e) registering signals from nonselected images with the signals from the secondary image, wherein said nonselected images are obtained from the image cycle from which the primary image was obtained;

(f) registering signals from remaining images in the subset with signals from the primary image, so as to determine the location of the signals depicted in the images with respect to each other, thereby producing signal clumps; and
(g) selecting a signal from each of said signal clumps, thereby forming a template that permits the identification of the locations of features of said specimen.

12. An imaging system comprising:
(a) a detector;
(b) at least one storage capacity; and
(c) a processor configured for
(i) transferring image data from the detector to the at least one storage capacity,
(ii) analyzing the image data to produce analyzed data, wherein the analyzing of the image data set comprises registering multiple image data sets to a template and identifying a different characteristic of a feature between two or more images, and
(iii) transferring the analyzed data to the at least one storage capacity,

wherein the p

Assignees

• Garcia Francisco
• Maisinger Klaus
• Tanner Stephen
• Moon John
• Mann Tobias
• Parkinson Michael Lawrence
• Cox Anthony James
• Ge Haifang H
• Illumina Inc

Inventors

• Garcia Francisco
• Maisinger Klaus
• Tanner Stephen
• Moon John
• Mann Tobias
• Parkinson Michael Lawrence
• Cox Anthony James
• Ge Haifang H

Classifications

• G06T7/246

  using feature-based methods, e.g. the tracking of corners or segments · CPC title

• G06T7/33

  using feature-based methods · CPC title

• G06T2207/30024

  Cell structures in vitro; Tissue sections in vitro · CPC title

• G06T7/337

  involving reference images or patches · CPC title

• G06T7/248

  involving reference images or patches · CPC title