A dynamic positioning method for high-density gene chip pore positions

Abstract

The present invention provides a dynamic positioning method for the hole positions of a high-density gene chip, which comprises: step S1: solidifying the relative position relationship between the hole positions on any high-density memory chip scanning diagram to obtain a positioning point matrix; step S2: inputting the scanning diagram of the high-density gene chip to be tested into the coordinate system and fixing it, and solving the inclination angle of the scanning diagram of the high-density gene chip to be tested by the Fourier transform method; step S3: adjusting the positioning point matrix as a whole to the same inclination angle as the scanning diagram of the high-density gene chip to be tested; step S4: continuously iterating the position algorithm of the positioning point matrix as a whole until the hole position to be tested coincides with the positioning point; step S5: the position of the hole position to be tested on the high-density gene chip to be tested is the current position of the positioning point that coincides with it in the current positioning point matrix. The positioning algorithm of the present application is simple, the number of iterations is small, the positioning efficiency is high, and the positioning accuracy is high.

Description

Technical Field

[0001] The invention relates to the technical field of biological detection, and in particular to a method for positioning holes in a high-density gene chip. Background Art

[0002] The traditional gene chip well positioning method requires positioning each bead one by one. This well positioning mode increases the probability of error and does not make good use of the fixed position relationship between our wells. This may eventually lead to positioning failure. Summary of the invention

[0003] In order to overcome the above technical defects and increase the success rate of well positioning, the present invention provides a dynamic positioning method for high-density gene chip wells, wherein the well positions on each high-density gene chip to be tested are fixed and follow the same arrangement rule, and the dynamic positioning method comprises:

[0004] Step S1: solidify the relative position relationship between the holes on any high-density memory chip scan map to obtain a positioning point matrix, and copy the positioning point matrix to the coordinate system, the positioning point matrix is ​​composed of a number of positioning points, and the number of positioning points and the positioning point arrangement rule of the positioning point matrix are respectively the same as the number of holes and the hole arrangement rule in the high-density memory chip scan map;

[0005] Step S2: inputting the scanned image of the high-density gene chip to be tested into the coordinate system and fixing it, and using the Fourier transform method to solve the tilt angle of the scanned image of the high-density gene chip to be tested;

[0006] Step S3: adjusting the entire matrix of positioning points to the same tilt angle as the scanned image of the high-density gene chip to be tested;

[0007] Step S4: continuously iterating the position algorithm of the entire positioning point matrix until the hole position to be measured coincides with the positioning point, and then stopping the dynamic movement of the entire positioning point matrix;

[0008] Step S5: Obtain the horizontal coordinate and vertical coordinate of any positioning point in the current positioning point matrix, and further obtain the current position of all positioning points in the current positioning point matrix by combining the positioning point arrangement rule and the overall tilt angle of the positioning point matrix. The position of the well to be tested on the high-density gene chip to be tested is the current position of the positioning point that coincides with it.

[0009] Furthermore, in step S2, after the image is transformed into the frequency domain, for each point in the centered frequency domain image, its brightness represents the amplitude of the plane wave, and the direction from the midpoint of the image to it is the direction of the plane wave, that is, the tilt angle of the scanned image of the high-density gene chip to be tested.

[0010] Further, in step S4, after each position iteration of the entire positioning point matrix, a circular area is selected with each positioning point in the positioning point matrix as the center and the hole radius as the radius. The grayscale mean value of all pixels within the selected circular area is taken. When the sum of the grayscale mean values of the circular areas corresponding to all positioning points is the largest, it is determined that the to-be-detected hole positions on the high-density gene chip coincide with the positioning points.

[0011] Further, in step S5, the to-be-detected hole positions on the to-be-detected high-density gene chip are several hole positions within the region of interest in the scanned image of the to-be-detected high-density gene chip.

[0012] Further, in step S4, assuming that the resolution of the scanned image of the to-be-detected high-density gene chip is M×N, and the size of the region of interest is C×R, then the iteration range in the x-axis direction does not exceed M - C, and the iteration range in the y-axis direction does not exceed N - R.

[0013] Further, in order to minimize the number of iterations as much as possible, first, a large step size of half of the hole radius is used for iteration to find the coordinate region with a relatively high sum of grayscale values; subsequently, within the coordinate region with a relatively high sum of grayscale values found by the above large step size, a small step size of one pixel is used for iteration, so as to more accurately find the position when the sum of the grayscale mean values of the circular areas corresponding to all positioning points is the largest.

[0014] Further, in step S5, the abscissa and ordinate of the upper left positioning point in the current positioning point matrix are obtained.

[0015] Further, the arrangement rule of the hole positions on the to-be-detected high-density gene chip and the arrangement rule of the positioning points on the positioning point matrix are both rectangular point matrices with a specific distance between adjacent ones.

[0016] After adopting the above technical solution, compared with the prior art, the following beneficial effects are achieved:

[0017] This application uses the method of overall position iteration of the positioning point matrix to perform batch global positioning on the to-be-detected hole positions on the to-be-detected high-density gene chip. The positioning algorithm is simple, the number of iterations is small, the positioning efficiency is high, and the positioning accuracy is high. BRIEF DESCRIPTION OF THE DRAWINGS

[0018] Figure 1 is a schematic diagram of the principle of continuous position algorithm iteration of the entire positioning point matrix of this application. The light gray rectangular border in the figure is only a virtual border added for easy understanding;

[0019] Figure 2 is a schematic diagram of three parameters involved in the positioning point matrix of this application;

[0020] Figure 3The positioning effect diagram of high-density gene chip hole positions using the dynamic positioning method of the present application. Detailed implementation manners

[0021] The advantages of the present invention are further elaborated below in conjunction with the accompanying drawings and specific embodiments. Those skilled in the art should understand that the content specifically described below is illustrative rather than restrictive, and should not be used to limit the protection scope of the present invention.

[0022] This embodiment provides a dynamic positioning method for high-density gene chip hole positions, which is an image positioning algorithm for high-density gene chips. The dynamic positioning method includes steps S1 - S5:

[0023] Step S1: Fix the relative position relationship between the hole positions on any high-density memory chip scan image to obtain a positioning point matrix, and copy the positioning point matrix into the coordinate system.

[0024] Exemplarily, the iterative object described in this embodiment is a rectangular point matrix with N points (N is the number of hole positions in a high-density memory chip scan image). The hole positions on each high-density gene chip to be measured are fixed and follow the same arrangement rule. Exemplarily, the actual hole positions to be measured are several hole positions arranged in a honeycomb pattern in the region of interest in the rectangular high-density memory chip scan image. In this embodiment, the positions of all hole positions on the same scan image are fixed and follow the same honeycomb arrangement rule. Therefore, we can consider fixing the position relationship between all hole positions as a positioning point matrix. Then, for each high-density gene chip scan image to be measured, only need to move the positioning point matrix as a whole relative to the high-density gene chip scan image to be measured, and then the positions of all hole positions in each scan image can be matched, so as to realize batch positioning of the hole positions on the high-density gene chip scan image to be measured, without the need to separately find the coordinates of each hole position.

[0025] The positioning point matrix is composed of several positioning points. The number of positioning points and the positioning point arrangement rule of the positioning point matrix are the same as the number of hole positions and the hole position arrangement rule in the high-density memory chip scan image respectively. Exemplarily, the arrangement rule of the hole positions on the high-density gene chip to be measured and the arrangement rule of the positioning points on the positioning point matrix are both rectangular point matrices with a specific distance between adjacent ones.

[0026] Step S2: Input the high-density gene chip scan image to be measured into the coordinate system and fix it, and use the Fourier transform method to solve the tilt angle of the high-density gene chip scan image to be measured.

[0027] Before iteration, we need to ensure that our rectangular dot matrix has the same tilt angle as the actually scanned image. Otherwise, when shooting a high-density gene chip, if it is not placed correctly and the scanned image is tilted, we can never use a regular rectangle to accurately locate the microbeads on the tilted image. We use the Fourier transform method to find the tilt angle of the scanned image of the high-density gene chip to be measured: After transforming the image into the frequency domain, for each point in the centered frequency domain image, its brightness represents the amplitude of the plane wave, and the direction from the point in the image to it is the direction of the plane wave, which is also the tilt angle of the scanned image of the high-density gene chip to be measured.

[0028] Step S3: Adjust the entire positioning dot matrix to the same tilt angle as the scanned image of the high-density gene chip to be measured.

[0029] After obtaining the tilt angle of the scanned image of the high-density gene chip to be measured, rotate all the positioning dots in the entire positioning dot matrix by the corresponding angle so that our algorithm can better find the coordinate positions of each hole on the scanned image of the high-density gene chip.

[0030] Step S4: Continuously perform position algorithm iteration on the entire positioning dot matrix until the hole to be measured coincides with the positioning dot, and then stop the dynamic movement of the entire positioning dot matrix.

[0031] Suppose the resolution of the scanned image of the high-density gene chip to be measured is M×N, and the size of the region of interest is C×R. Then, in the x-axis direction (horizontal direction), the iteration range does not need to exceed M - C, and in the y-axis direction (vertical direction), the iteration range does not need to exceed N - R. In practice, the captured chip image will not be so close to the limit value. Therefore, according to practical experience, the iteration range can be appropriately reduced on this basis to obtain higher efficiency. An overly small iteration range may cause our optimal solution not to be within it; an overly large iteration range will result in a lot of unnecessary operations.

[0032] After correcting the angle of the positioning dot matrix and finding the iteration range, we can start to find the positions of all microbeads based on the gray value sum index. To minimize the number of iterations, first use a large step size (such as half of the hole radius) to iterate and find the coordinate region with a higher gray value sum; then, more accurately find the center coordinates of the holes in the coordinate region with a higher gray value sum found by the above large step size. For example, iterate with a small step size of 1 pixel to more accurately find the position where the gray value mean sum of the circular region corresponding to all positioning dots is the largest. As Figure 1 shown, continuously perform position algorithm iteration on the entire positioning dot matrix until the hole to be measured coincides with the positioning dot, and then stop the dynamic movement of the entire positioning dot matrix.

[0033] The entire positioning process can be regarded as a rectangle moving continuously on a picture with regularly arranged hole positions. In the positioning point matrix, N points with relatively fixed positions are preset (N is the number of hole positions in a high-density memory chip scan picture), and each point corresponds to the center of a hole position on a high-density memory chip. The index guiding the movement of this rectangular point matrix is to maximize the sum of the grayscale values of all points on this rectangular point matrix. In this way, the result obtained in this iteration is regarded as the optimal solution, and it is determined that the to-be-tested hole position coincides with the positioning point.

[0034] After each position iteration of the entire positioning point matrix, taking each positioning point in the positioning point matrix as the center and the hole position radius as the radius, a circular area is selected. The average grayscale value of all pixels within the selected circular area is taken. When the sum of the average grayscale values of the circular areas corresponding to all positioning points is the largest, it is determined that the to-be-tested hole position of the high-density gene chip coincides with the positioning point. Specifically, after each position iteration of the rectangular point matrix, each positioning point on it corresponds to the center point of a located hole position. We take the positioning point as the center and R as the radius (R is the hole position radius, which can be measured in advance according to the scan picture of the to-be-tested high-density gene chip) to select a circular area, and take the average grayscale value of all pixels within the area as the grayscale value of the hole position. Since the grayscale value of the hole position area of the microbead must not be lower than that of the hole position area without microbeads (even if it is a completely signal-free microbead, it will be consistent with the background grayscale value), therefore, once the coordinates obtained by positioning are offset, the circular area for extracting features we obtain will include the grayscale value of a part of the background area of the scan picture of the to-be-tested high-density gene chip, resulting in a decrease in the grayscale value of the hole position we obtain. In this case, the coordinates of all hole positions corresponding to the highest overall grayscale value are the most accurate hole position coordinates. These two are mutually sufficient and necessary conditions.

[0035] Step S5: Obtain the abscissa and ordinate of any positioning point in the current positioning point matrix, and further combine the positioning point arrangement rule and the inclination angle of the entire positioning point matrix to obtain the current positions of all positioning points in the current positioning point matrix. Then, the position of the to-be-tested hole position on the to-be-tested high-density gene chip is the current position of the positioning point that coincides with it.

[0036] Exemplarily, as Figure 2 shown, in order to minimize the complexity of algorithm iteration as much as possible, only three variables (the abscissa of the top-leftmost positioning point of this rectangular point matrix, the ordinate of the top-leftmost positioning point of this rectangular point matrix, the inclination angle of the entire rectangular point matrix) are used to describe the parameters of the rectangular point matrix. At the same time, taking the sum of the grayscale values corresponding to all positioning points in the rectangular point matrix as the largest as the solution index, so as to move the entire rectangular point matrix to a suitable position. Each positioning point therein can correspond to the coordinate position of the center of a hole position on the high-density gene chip in the scan picture. Thus, we have completed the positioning of the hole positions in the high-density gene chip. The positioning effect example is asFigure 3 As shown, the "+" in the figure represents the center position of the hole found by the positioning algorithm. It can be seen that the dynamic positioning algorithm we proposed accurately found the center position of the hole to be measured and successfully completed the hole positioning task.

[0037] It should be noted that the embodiments of the present invention have better implementability and are not in any form a limitation on the present invention. Any person skilled in the art may use the technical content disclosed above to change or modify it into an equivalent effective embodiment. However, as long as it does not depart from the content of the technical solution of the present invention, any modification, equivalent change or modification made to the above embodiments based on the technical essence of the present invention still falls within the scope of the technical solution of the present invention.

Claims

1. A dynamic positioning method for the pore positions of a high-density gene chip, characterized in that, the pore positions on each high-density gene chip to be measured are fixed and follow the same arrangement rule, and the dynamic positioning method includes: Step S1: Fix the relative position relationship between the pore positions on a scanned image of any high-density memory chip to obtain a positioning point matrix, and copy the positioning point matrix into a coordinate system. The positioning point matrix is composed of several positioning points, and the number of positioning points and the arrangement rule of the positioning points in the positioning point matrix are the same as the number of pore positions and the pore position arrangement rule in the scanned image of the high-density memory chip respectively; Step S2: Input the scanned image of the high-density gene chip to be measured into the coordinate system and fix it. Use the Fourier transform method to solve the tilt angle of the scanned image of the high-density gene chip to be measured; Step S3: Adjust the whole positioning point matrix to the same tilt angle as the scanned image of the high-density gene chip to be measured; Step S4: Continuously perform position algorithm iteration on the whole positioning point matrix until the pore position to be measured coincides with the positioning point, and then stop the dynamic movement of the whole positioning point matrix; Step S5: Obtain the abscissa and ordinate of any positioning point in the current positioning point matrix, and further combine the positioning point arrangement rule and the tilt angle of the whole positioning point matrix to obtain the current positions of all positioning points in the current positioning point matrix. Then, the position of the pore position to be measured on the high-density gene chip to be measured is the current position of the positioning point that coincides with it; In step S4, after each position iteration of the whole positioning point matrix, take a circular area with each positioning point in the positioning point matrix as the center and the pore radius as the radius, and take the gray level mean value of all pixels in the selected circular area. When the sum of the gray level mean values of the circular areas corresponding to all positioning points is the largest, it is determined that the pore position to be measured of the high-density gene chip coincides with the positioning point.

2. The dynamic positioning method for the pore positions of a high-density gene chip according to claim 1, characterized in that, in step S2, after the image is transformed to the frequency domain, for each point in the frequency domain image after centering, its brightness represents the amplitude of the plane wave, and the direction from the point in the image to it is the direction of the plane wave, that is, the tilt angle of the scanned image of the high-density gene chip to be measured.

3. The dynamic positioning method for the pore positions of a high-density gene chip according to claim 1, characterized in that, in step S5, the pore positions to be measured on the high-density gene chip to be measured are several pore positions within the region of interest in the scanned image of the high-density gene chip to be measured.

4. The dynamic positioning method for the pore positions of a high-density gene chip according to claim 3, characterized in that, in step S4, assuming that the resolution of the scanned image of the high-density gene chip to be measured is M×N, and the size of the region of interest is C×R, then the iteration range in the x-axis direction does not exceed M - C, and the iteration range in the y-axis direction does not exceed N - R.

5. The dynamic positioning method for the pore positions of a high-density gene chip according to claim 4, characterized in that, First, iterate with a large step size equal to half of the hole radius to find the coordinate region with a higher sum of gray values. Subsequently, in the coordinate region with a higher sum of gray values found by the above large step size, iterate with a small step size of one pixel to more precisely find the position when the sum of the gray values of the circular regions corresponding to all positioning points is the largest.

6. The dynamic positioning method for high-density gene chip hole positions according to claim 1, characterized in that, in step S5, the abscissa and ordinate of the upper left positioning point in the current positioning point matrix are obtained.

7. The dynamic positioning method for high-density gene chip hole positions according to claim 1, characterized in that, the arrangement rules of the hole positions on the high-density gene chip to be measured and the arrangement rules of the positioning points on the positioning point matrix are both rectangular point matrices with a specific distance between adjacent ones.

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