Image analysis system and method of biochip

• US 20030072476A1
• Filed: 10/10/2002
• Published: 04/17/2003
• Est. Priority Date: 10/11/2001
• Status: Active Grant

• Current Assignee: Industry-University Cooperation Foundation Hangyang University
• Original Assignee: Industry-University Cooperation Foundation Hangyang University
• Inventors: Kim, Jin Hyuk, Lee, Yong Sung, Lee, Young Seek
• Granted Patent: US 7,085,404 B2
• Time in Patent Office: Days
• US Class Current: 382/128
• CPC Class Codes: G06T 7/60 Analysis of geometric attributes

Abstract

Disclosed is a biochip image analysis system which comprises an image storage unit for storing images including an original image of a biochip comprising a set of specific genes expressed in different environments by fluorescent bases of different colors; an image converter for converting the original image into a test image, forming an overlapped image and a color image, and storing the images in the image storage unit; an edge detector for separating the spot-formed genes from the test image, generating spot and background templates, and detecting an edge to measure expression degrees of the genes; a data processor for generating statistical data using the spot and background templates, and performing luminance correction; and a data storage unit for storing the statistical data.

Claims

1. A biochip image analysis system comprising:

an image storage unit for storing various categories of image information including an original image of a biochip comprising a set of specific genes each expressed in different environments by fluorescent bases of different colors;

an image converter for converting the biochip'"'"'s original image stored in the image storage unit into a test image, forming an overlapped image and a color image from the test image, and storing the images in the image storage unit;

an edge detector for separating the genes in the spot form from the test image stored in the image storage unit, generating a spot template and a background template, and detecting an edge so as to measure expression degrees of the respective genes;

a data processor for generating statistical data on the basis of the spot template and the background template generated through the image storage unit and the edge detector, and performing luminance correction; and

a data storage unit for storing the statistical data generated by the data processor.

2. The system of claim 1, comprising an input/output unit for outputting the image or the data stored in the image storage unit, the edge detector, and the data storage unit to a screen according to a request by a user.

3. A biochip image analysis method, comprising:

(a) extracting an original image according to a fluorescent base from a biochip comprising a set of specific genes each expressed in a different environment by a fluorescent base of a different color;

(b) converting the original image into a test image, and extracting an overlapped image and a color image from the test image;

(c) respectively separating the genes in the spot form from the test image, generating a spot template and a background template including an area within a predetermined distance excluding the spot, and detecting an edge; and

(d) outputting statistical data on the basis of the spot template and the background template generated in (b) or (c), and performing luminance correction.

4. The method of claim 3, comprising (e) displaying the images and the data generated in (b) to (d) to a screen according to a request by a user.

5. The method of claim 3, wherein in (b), the original image has a 16-bit file format, and the original image is converted into an 8-bit test image so as to increase an image processing speed and output the original image to the user through a screen.

6. The method of claim 3, wherein in (b), the test image is colored in different pseudo-colors according to fluorescent bases, and is overlapped to generate a color image, and an overlapped image is generated using the pixels having greater values from among the pixels at the identical location of the test image.

7. The method of claim 3, wherein (c) comprises:

a segmentation step for separating respective spots from the test image in the spot format to generate a spot segment coordinate;

an edge detection step for extracting a spot segment of an n^th coordinate from the segmentation step to generate a spot edge and a background edge;

a template generation step for transplanting the spot edge and the background edge generated in the edge detection step onto an empty template, and detecting an edge on a subsequent coordinate'"'"'s spot segment; and

a termination step for terminating the generation of a spot template and a background template when the edge detection of all coordinates is generated in the segmentation step.

8. The method of claim 3, wherein (c) comprises:

an enhancement step for enhancing the luminance of the test image to emphasize the edge;

a comparison step for comparing a previously established critical value with a mean value of a predetermined number of pixels from the edge emphasized in the enhancement step, to generate an edge;

an effective edge extraction step for removing edges under a reference size from the edges detected in the comparison step, and connecting partially opened edges by the shortest distance; and

a template storage step for generating a spot template and a background template comprising the edges extracted in the effective edge extraction step, and storing the spot template and the background template.

9. The method of claim 3, wherein (c) comprises:

a reference template generation step for generating a reference template on the center of which a reference circle is formed on the basis of a mean size of the spots from the test image;

an enhancement step for enhancing the luminance of the test image to emphasize the edge;

a comparison step for comparing a previously established critical value with a mean value of a predetermined number of pixels from the edge emphasized in the enhancement step, to generate an edge;

an effective edge extraction step for removing edges under a reference size from the edges detected in the comparison step, and connecting partially opened edges by the shortest distance to generate an effective edge template; and

a template storage step for synthesizing the effective edge template and the reference template to generate a spot template, synthesizing the inverted effective edge template and the inverted reference template to generate a background template, and storing the spot template and the background template.

10. The method of claim 8, wherein the comparison step comprises a smoothing step for reducing the gradient of the edge emphasized in the enhancement step to extract effective edges.

11. The method of claim 9, wherein the comparison step comprises a smoothing step for reducing the gradient of the edge emphasized in the enhancement step to extract effective edges.

12. The method of claim 3, wherein in (d), various measured values including a mean value, a standard deviation, a central value, a mode, a spot'"'"'s area and circumference, a number of holes in the spot, and a fragmentation state are stored as statistical data on the basis of the spot template and the background template.