CN113670865B - Resolution board, resolution evaluation method and related equipment - Google Patents

Resolution board, resolution evaluation method and related equipment Download PDF

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CN113670865B
CN113670865B CN202010403747.7A CN202010403747A CN113670865B CN 113670865 B CN113670865 B CN 113670865B CN 202010403747 A CN202010403747 A CN 202010403747A CN 113670865 B CN113670865 B CN 113670865B
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CN113670865A (en
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伯恩
徐洪
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MGI Tech Co Ltd
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Abstract

The present invention provides a resolution plate comprising: the resolution test image comprises a plurality of sites which are symmetrical in center, and the distance between every two adjacent sites in the same direction gradually increases from the center point to the outside. The invention also provides a method for evaluating the resolution by using the resolution plate, a gene sequencing system, a gene sequencer and a computer readable storage medium. By using the embodiment of the invention, the efficiency and the robustness of resolution evaluation can be improved.

Description

Resolution board, resolution evaluation method and related equipment
Technical Field
The invention relates to the technical field of image processing, in particular to a resolution board, a resolution evaluation method, a gene sequencing system, a gene sequencer and a storage medium.
Background
Gene sequencing refers to analysis of the base sequence of a particular DNA fragment, i.e., the arrangement of adenine (A), thymine (T), cytosine (C) and guanine (G). One of the sequencing methods currently in common use is: the four bases respectively carry different fluorescent groups, and the different fluorescent groups emit fluorescence with different wavelengths (colors) after being excited, so that the types of synthesized bases can be identified by identifying the fluorescence wavelengths, and the base sequence is read. The second generation sequencing technology adopts a high resolution microscopic imaging system, photographs and collects fluorescent molecular images of DNA nanospheres (DNB, DNANanoballs) on a biochip (gene sequencing chip), and sends the fluorescent molecular images into base recognition software to read image signals so as to obtain base sequences. The imaging quality of the microscopic imaging link of the gene sequencer has a great influence on the accuracy of base identification, and the resolution of a microscopic imaging system directly influences the imaging quality.
In the prior art, the resolution evaluation method mainly comprises a direct observation method and an ESF/MTF method, wherein the direct observation method determines the resolution of an imaging system by observing whether the intensity values of adjacent lines of a line pair can be separated; the ESF/MTF method determines the resolution of the imaging system by calculating the ESF (EDGESPREAD FUNCTION ) and MTF (Modulation Transfer Function) of the hypotenuse trapezoid. However, neither of the above methods directly evaluates whether neighboring DNA nanospheres are distinguishable, and both methods are greatly affected by environmental factors, resulting in low resolution evaluation efficiency.
Disclosure of Invention
In view of the foregoing, it is necessary to provide a resolution plate, a resolution evaluation method, a gene sequencing system, a gene sequencer, and a storage medium capable of improving the efficiency and robustness of resolution evaluation for the case of small molecular size and small pitch of DNA nanospheres and/or biomacromolecules.
A first aspect of an embodiment of the present invention provides a resolution plate, including: the resolution test image comprises a plurality of sites which are symmetrical in center, and the distance between every two adjacent sites in the same direction gradually increases from the center point to the outside.
Further, in the resolution plate provided by the embodiment of the invention, the sites are in a central symmetrical pattern, and the distances between adjacent sites in the same direction are increased in an arithmetic progression from the central point.
The second aspect of the embodiment of the present invention further provides a method for performing resolution evaluation by using the resolution board described in any one of the foregoing embodiments, where the method is applied to an optical imaging system, and the method for resolution evaluation includes:
Collecting an image to be analyzed of the resolution plate;
calculating an intensity function of the image to be analyzed;
performing fast Fourier transform according to the intensity function to obtain a target frequency spectrum of the image to be analyzed;
Determining the number of target spectrum peaks contained in the target spectrum;
Traversing a preset mapping table according to the number of the target spectrum peaks to obtain a resolution value of the optical imaging system.
Further, in the above resolution evaluation method provided by the embodiment of the present invention, the performing fast fourier transform according to the intensity function to obtain the target spectrum of the image to be analyzed includes:
Acquiring a first image of the image to be analyzed along a preset direction;
calculating a one-dimensional intensity function of the first image;
And executing one-dimensional fast Fourier transform according to the one-dimensional intensity function to obtain a first target frequency spectrum of the first image.
Further, in the above resolution evaluation method provided by the embodiment of the present invention, the method further includes:
when the number of the preset directions is greater than 1, respectively acquiring a first image set of the image to be analyzed along the preset directions;
calculating a one-dimensional intensity function of each image in the first image set to obtain a one-dimensional intensity function set;
Calculating an average value according to each one-dimensional intensity function in the one-dimensional intensity function set to obtain a one-dimensional average intensity function;
And executing one-dimensional fast Fourier transform according to the one-dimensional average intensity function to obtain a first target frequency spectrum of the first image set.
Further, in the above resolution evaluation method provided by the embodiment of the present invention, the performing fast fourier transform according to the intensity function to obtain the target spectrum of the image to be analyzed further includes:
Calculating a two-dimensional intensity function of the image to be analyzed;
And executing two-dimensional fast Fourier transform according to the two-dimensional intensity function to obtain a second target frequency spectrum of the image to be analyzed.
Further, in the above resolution evaluation method provided by the embodiment of the present invention, the determining the number of target spectrum peaks included in the target spectrum includes:
Acquiring a resolvable region corresponding to the target frequency spectrum;
Calculating a maximum value of the number of spectral peaks contained in the distinguishable region;
and determining the maximum value as a target frequency spectrum peak number.
A third aspect of embodiments of the present invention also provides a gene sequencing system comprising:
The image acquisition module is used for acquiring an image to be analyzed of the resolution board;
The function calculation module is used for calculating the intensity function of the image to be analyzed;
the frequency spectrum acquisition module is used for executing fast Fourier transform according to the intensity function to obtain a target frequency spectrum of the image to be analyzed;
the quantity determining module is used for determining the quantity of target spectrum peaks contained in the target spectrum;
And the resolution determining module is used for traversing a preset mapping table according to the number of the target spectrum peaks to obtain a resolution value of the optical imaging system.
A fourth aspect of the embodiments of the present invention also provides a gene sequencer comprising a processor for implementing the steps of the resolution assessment method according to any one of the preceding claims when executing a computer program stored in a memory.
A fifth aspect of the embodiments of the present invention also provides a computer-readable storage medium having stored thereon a computer program which, when executed by a processor, implements the steps of the resolution evaluation method of any one of the above.
The embodiment of the invention provides a resolution board, a resolution evaluation method, a gene sequencing system, a gene sequencer and a computer readable storage medium, and aims at the conditions of small molecular size and small spacing of DNA nanospheres and/or biomacromolecules and the like, and designs a resolution board with the spacing of adjacent sites gradually becoming larger from a central point outwards. In addition, the invention can improve the resolution evaluation capability by carrying out the fast Fourier transform on the space domain and counting the number of the spectrum peaks in the frequency domain.
Drawings
Fig. 1 is a schematic diagram of a resolution plate provided by an embodiment of the present invention.
Fig. 2 is a flowchart of a resolution evaluation method according to an embodiment of the present invention.
Fig. 3a is a schematic diagram of a design pattern of a resolution plate according to an embodiment of the present invention.
Fig. 3b is a schematic diagram of a resolution plate image acquired by an optical imaging system according to an embodiment of the present invention.
Fig. 3c is a schematic diagram of an intensity function in a spatial domain according to an embodiment of the present invention.
Fig. 3d is a schematic diagram of a one-dimensional fourier spectrum of the intensity function of fig. 3c in the frequency domain.
Fig. 3e is a schematic diagram of a two-dimensional fourier spectrum corresponding to fig. 3 b.
Fig. 3f is a schematic diagram of a one-dimensional spectrum of the dashed box portion in fig. 3 e.
Fig. 4 is a schematic diagram of a preset mapping table according to an embodiment of the present invention.
FIG. 5 is a schematic diagram of a gene sequencer according to an embodiment of the present invention.
FIG. 6 is a functional block diagram of an example of the gene sequencer shown in FIG. 5.
The invention will be further described in the following detailed description in conjunction with the above-described figures.
Detailed Description
In order that the above-recited objects, features and advantages of the present application will be more clearly understood, a more particular description of the application will be rendered by reference to specific embodiments thereof which are illustrated in the appended drawings. It should be noted that, without conflict, the embodiments of the present application and features in the embodiments may be combined with each other.
In the following description, numerous specific details are set forth in order to provide a thorough understanding of the present invention, the described embodiments are examples of some, but not all, embodiments of the invention. All other embodiments, which can be made by those skilled in the art based on the embodiments of the invention without making any inventive effort, are intended to be within the scope of the invention.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The terminology used herein in the description of the invention is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention.
Referring to fig. 1, fig. 1 (a), (b), (c), (d), (e), (f), (g), (h) and (i) are schematic diagrams of a resolution plate according to an embodiment of the invention. The resolution plate can be designed aiming at the characteristics that the molecular size of biological macromolecules in molecular fluorescence detection and/or DNA nanospheres in a gene sequencer is smaller and the molecular size is arranged regularly, and the resolution is determined by evaluating the minimum distance which can be resolved by an optical imaging system. The molecular fluorescence detection is an ultrasensitive detection technology, and single or multiple molecules can be detected and imaged in a medium such as a solution, so that the way of chemical reaction is monitored in real time, and particularly biological macromolecules are detected and information between the molecular structure and the function is provided, including gene sequencing analysis.
As shown in fig. 1, the resolution plate includes: the device comprises a substrate and a resolution test image arranged on the substrate, wherein the resolution test image (an image formed by white sites of each figure in fig. 1 is the resolution test image) consists of a plurality of sites which are centrosymmetric, and the distance between every two adjacent sites in the same direction gradually increases from the central point to the outside. Wherein the resolution test image may be a dot column pattern. The boundaries of the resolution test images are not limited (the peripheral border of each of the figures in fig. 1 is merely exemplary), and may be set according to actual requirements. It can be understood that the resolution test image is designed to be composed of a plurality of points which are symmetrical in center, on one hand, because the pattern which is symmetrical in center can accommodate the same points on four branches, and the total points are the most, the points of the four branches can be ensured to be used for subsequent analysis, and the robustness is better (if the resolution test image is not symmetrical in center, the pattern can only obtain more points in a few directions, and meanwhile, the points on some branches are too few, and the branches cannot be used for subsequent algorithms); on the other hand, the optical imaging system has the best imaging quality in the center of the field of view, so the center of the resolution test image is placed in the center of the field of view, and denser points are imaged by using the center of the field of view.
In an embodiment of the present invention, the sites are in a central symmetrical pattern, for example, the sites may be one of circles, squares, regular triangles, regular hexagons and regular octagons. The locus extends outwardly from the central point in a horizontal and/or vertical direction. The spacing between adjacent sites in the same direction increases in an arithmetic progression from the center point. The materials of the substrate may include: optical glass, fused quartz, optical ceramic material and silicon wafer.
In at least one embodiment of the present invention, the maximum number of points M and N of the center point (including the center point) of the resolution test image outward in the horizontal direction and/or the vertical direction are acquired, respectively.And/>Adjacent site spacing in the horizontal and vertical directions from the center point of the resolution test image, respectively, where n x and n y are integers, and n x∈[1,M-1],ny e [1, n-1].
In at least one embodiment of the present invention, in designing the resolution plate, it is assumed that the resolution of the optical imaging system in the x, y directions is R x and R y, respectively, and the pitch between adjacent sites is equal to the pitch between adjacent sitesAnd/>Arranged in an arithmetic progression. It can be appreciated that when/>And/or/>When the two points are not resolved by the optical imaging system. That is, by judging which two adjacent sites cannot be separated by the optical imaging system, the resolution of the optical imaging system can be evaluated.
An embodiment of the present invention provides a resolution board, including: the resolution test image comprises a plurality of sites which are symmetrical in center, and the distance between every two adjacent sites in the same direction gradually increases from the center point to the outside. The invention designs a resolution board aiming at the characteristics of small molecular size of biological macromolecules in molecular fluorescence detection and/or DNA nanospheres in a gene sequencer and regular arrangement, and well simulates an ideal environment of an optical imaging system based on the biological macromolecules or the DNA nanospheres, thereby effectively evaluating the resolution.
Fig. 2 is a flowchart of a resolution evaluation method according to an embodiment of the present invention. The resolution evaluation method can be used for resolution evaluation by using the resolution plate, and can be used in an optical imaging system. As shown in fig. 2, the resolution evaluation method may include the steps of:
S21, acquiring an image to be analyzed of the resolution plate.
In at least one embodiment of the present invention, referring to fig. 3a, the shape of the sites is circular, the site diameter d=500 nm, m=n=28, Taking an arithmetic series, the substrate is made of silicon, the resolution test image is a resolution plate with a "+" pattern in the graph (g) in fig. 1 as an example, and the optical imaging system is called to collect the resolution plate to obtain an image to be analyzed of the resolution plate, as shown in fig. 3b, fig. 3b is a schematic diagram of the image of the resolution plate collected by the optical imaging system according to an embodiment of the present invention.
S22, calculating an intensity function of the image to be analyzed.
In at least one embodiment of the present invention, the intensity function is a relationship function between position information of a pixel point in the image to be analyzed and a brightness value corresponding to the pixel point. The pixel point can be understood as a minimum image unit identifiable by the optical imaging system, the position information of the pixel point and the corresponding brightness value of the pixel point can be determined, and the position information of the pixel point can include position information along the x and y directions. The step of calculating an intensity function of the image to be analyzed may comprise: acquiring position information (x, y) of the pixel points; acquiring a brightness value corresponding to the pixel point; and determining a functional relation between the position information and the brightness value, wherein the functional relation is the intensity function of the image to be analyzed.
In at least one embodiment of the present invention, the intensity function includes a one-dimensional intensity function and a two-dimensional intensity function. Illustratively, the one-dimensional intensity function is denoted as f (x, y 0), abbreviated as f (x), where y 0 is a constant, and can be set according to the actual requirement; the two-dimensional intensity function is denoted as f (x, y).
S23, performing fast Fourier transform according to the intensity function to obtain a target frequency spectrum of the image to be analyzed.
In at least one embodiment of the present invention, the spacing between adjacent sites in the horizontal and vertical directions in the spatial domainAnd/>The point columns are arranged in an arithmetic progression, the distance between adjacent points corresponds to the period of the signal, and the distance value is different, so that the corresponding frequencies in the frequency domain are different, a plurality of relatively sparse frequency spectrum peaks with different frequencies are formed, and two adjacent points which are relatively dense in the space domain are more easily distinguished in the frequency spectrum domain. And the spacing of adjacent sites in the spatial domainAnd/>The number of the frequency spectrum peaks in the frequency spectrum domain is consistent with that of the frequency spectrum peaks, so that by counting the number of the frequency peaks, the two adjacent sites in the space domain can be judged to be distinguishable, and the resolution of the optical imaging system is evaluated.
In at least one embodiment of the present invention, the number of spectral peaks in the frequency domain can be one-to-one corresponding to the number of different pitches of adjacent sites in the spatial domain by space-to-frequency conversion (i.e., fast fourier transform). The fast fourier transform includes a one-dimensional fast fourier transform and a two-dimensional fast fourier transform.
Specifically, when the fast fourier transform includes a one-dimensional fast fourier transform, the performing the fast fourier transform according to the intensity function to obtain the target spectrum of the image to be analyzed includes: acquiring a first image of the image to be analyzed along a preset direction; calculating a one-dimensional intensity function of the first image; and executing one-dimensional fast Fourier transform according to the one-dimensional intensity function to obtain a first target frequency spectrum of the first image.
The preset direction is preset by a tester, and may be 1 direction or multiple directions, which is not limited herein. Said performing a one-dimensional fast fourier transform from said one-dimensional intensity function comprises: inputting the one-dimensional intensity function into formula (1):
Wherein F 1D (u) represents a one-dimensional fourier transform of F (x), F (x) is a one-dimensional intensity function along the x direction, the subscript 1D represents one dimension, u is a frequency variable corresponding to the x direction, and P is the number of pixels of the image to be analyzed along the x direction. In an embodiment, f (x) is a shorthand of f (x, y 0), y 0 =q/2 (representing selecting a row of intensity values right in the middle of the y axis), Q is the number of pixels of the image to be analyzed along the y direction.
Illustratively, for a resolution board in which the resolution test image is a "+" type pattern of the graph (g) of fig. 1, one branch is along the x or y direction, and the image corresponding to the branch is the first image, as shown by the dashed box in fig. 3 b. The one-dimensional intensity function of the first image is calculated, as shown in fig. 3c, and fig. 3c is a schematic diagram of the intensity function in the spatial domain according to an embodiment of the present invention. And performing one-dimensional fast Fourier transform according to the one-dimensional intensity function to obtain a first target frequency spectrum of the first intensity image, as shown in FIG. 3d, and FIG. 3d is a schematic diagram of a one-dimensional Fourier frequency spectrum of the intensity function in the frequency domain in FIG. 3 c.
As can be seen from an examination of fig. 3c, in the spatial domain, the arrangement of peaks (from left to right) becomes progressively denser from sparse, and adjacent peaks will overlap to form peaks of higher amplitude and narrower width. When adjacent peaks are densified to some extent, the superimposed peaks become insignificant (but still present), resulting in inaccuracy in the resolved evaluation. In FIG. 3c, there are 22 peaks in total from left to right (the number of peaks in the spatial domain can be marked with numbers), corresponding toTherefore, by directly counting peaks in the spatial domain, traversing the preset mapping table according to the number of peaks in the spatial domain, and obtaining the resolution value of the optical imaging system in the x direction, namely 750. The preset mapping table is a factory preset value, and as shown in fig. 4, the preset mapping table includes mapping relations of a spatial domain point sequence number, a spatial domain adjacent site distance, a frequency spectrum peak number and resolution of an optical imaging system.
As can be seen from an examination of fig. 3d, there are 24 significant spectral peaks in the frequency domain from left to right (from low frequency to high frequency). Since the spectral peaks correspond to different frequencies, the different frequencies correspond to different periods, the different periods correspond to different adjacent point spacings in the spatial domain, wherein the low frequency spectral peaks correspond to larger adjacent point spacings and the high frequency spectral peaks correspond to smaller adjacent point spacings. Since there are 24 spectral peaks from low to high (the number of peaks in the frequency domain can be marked with numbers), the corresponding adjacent point spacing isTherefore, by directly counting peaks in a frequency domain, traversing a preset mapping table according to the number of peaks in the frequency domain, and obtaining the resolution value of the optical imaging system in the x direction, namely 650nm.
Therefore, by adopting the resolution evaluation method provided by the embodiment of the invention, the method for performing fast Fourier transform on the spatial domain is adopted to count the number of spectrum peaks in the frequency domain, so that the resolution evaluation capability can be improved.
In at least one embodiment of the present invention, the image to be analyzed may have a "defect" due to the quality of the resolution plate, and for such a problem, the intensity values of multiple branches may be selected to be weighted and averaged, and then one-dimensional fourier transformed. Specifically, the method further comprises: when the number of the preset directions is greater than 1, respectively acquiring a first image set of the image to be analyzed along the preset directions; calculating a one-dimensional intensity function of each image in the first image set to obtain a one-dimensional intensity function set; calculating an average value according to each one-dimensional intensity function in the one-dimensional intensity function set to obtain a one-dimensional average intensity function; and executing one-dimensional fast Fourier transform according to the one-dimensional average intensity function to obtain a first target frequency spectrum of the first image set.
In at least one embodiment of the present invention, when the fast fourier transform includes a two-dimensional fast fourier transform, the performing the fast fourier transform according to the intensity function to obtain the target spectrum of the image to be analyzed includes: calculating a two-dimensional intensity function of the image to be analyzed; and executing two-dimensional fast Fourier transform according to the two-dimensional intensity function to obtain a second target frequency spectrum of the image to be analyzed.
Unlike the one-dimensional fast fourier transform, the two-dimensional fourier transform method does not need to pick different branches of the resolution plate, but directly performs the two-dimensional fast fourier transform on the two-dimensional intensity function of the resolution plate. Specifically, the performing a two-dimensional fast fourier transform according to the two-dimensional intensity function comprises: inputting the two-dimensional intensity function to equation (2):
Wherein F 2D (u, v) represents the two-dimensional fourier transform of F (x, y), F (x, y) is a two-dimensional intensity function, subscript 2D represents two dimensions, u is a frequency variable corresponding to the x-direction, v is a frequency variable corresponding to the y-direction, P is the number of pixels of the image to be analyzed along the x-direction, and Q is the number of pixels of the image to be analyzed along the y-direction.
For the resolution board with the resolution test image being the "+" pattern of the graph (g) in fig. 1, as shown in fig. 3e, fig. 3e is a schematic diagram of a two-dimensional fourier spectrum corresponding to fig. 3b, where the two-dimensional fourier spectrum is "+" pattern. Here, to show the spectrum details, one branch of the two-dimensional fourier spectrum chart along the x-direction (as shown by the dashed box in fig. 3 e) is selected, and the spectrum amplitude is presented as shown in fig. 3f, and fig. 3f is a one-dimensional spectrum schematic diagram of the dashed box portion in fig. 3 e. As shown in FIG. 3f, there are 24 spectral peaks in the spectrum from left to right (from low frequency to high frequency), soThe resolution of the optical imaging system in the x-direction is 650nm. Similarly, a branch of the spectrogram along the y direction is selected, and the resolution of the optical imaging system in the y direction can be determined by counting the number of spectral peaks.
It will be appreciated that the benefit of using a two-dimensional fourier transform directly for the resolution plate is that, independent of the resolution plate's "drawbacks", accuracy determination can be achieved by counting the number of spectral peaks in the frequency domain.
S24, determining the number of target spectrum peaks contained in the target spectrum.
In at least one embodiment of the present invention, the target spectrum is divided into a resolvable region and an unresolved region, and the spectral peaks of the resolvable region are referred to as target spectral peaks. As shown in fig. 3d, there are higher frequency spectral peaks to the right of the 24 th spectral peak, but since they have smaller peaks and clutter interference, indicating that there is interference signal in the spatial domain and the spacing between this adjacent sites is the same, it is determined as an indistinguishable region. As shown in fig. 3c, 3d and 3f, the left side of the dotted line represents the resolvable region and the right side of the dotted line represents the unresolved region.
The determining the number of target spectrum peaks contained in the target spectrum comprises: acquiring a resolvable region corresponding to the target frequency spectrum; calculating a maximum value of the number of spectral peaks contained in the distinguishable region; and determining the maximum value as a target frequency spectrum peak number. Wherein, the calculating the maximum value of the number of the spectrum peaks in the distinguishable region can adopt direct observation of a spectrogram and count the spectrum peaks which are relatively smooth (without clutter interference); alternatively, machine learning or other methods may be used to count the number of spectral peaks.
And S25, traversing a preset mapping table according to the number of the target spectrum peaks to obtain a resolution value of the optical imaging system.
In at least one embodiment of the present invention, a preset mapping table is traversed according to the number of the target spectral peaks to obtain a resolution value of the optical imaging system. The preset mapping table comprises mapping relations of space domain point serial numbers, space domain adjacent site distances, frequency spectrum peak numbers and resolution of an optical imaging system. The space domain point sequence number and the space domain adjacent site distance are known in advance, and the frequency spectrum peak number and the resolution of the optical imaging system can be obtained through multiple times of calculation. It can be appreciated that the resolution of the optical imaging system can be estimated by traversing the preset mapping table, so that the resolution estimation efficiency can be improved.
It can be appreciated that in the existing method, when the resolution is evaluated, since the area of the image to be analyzed of the evaluation resolution is large, the image to be analyzed needs to be preprocessed, for example, uneven background is removed, etc. The non-uniform background is obtained mainly through low-pass filtering, on one hand, parameters of the low-pass filtering need to be adjusted repeatedly according to lighting conditions, and on the other hand, as the non-uniform background is difficult to obtain perfectly through adjusting the parameters of the low-pass filtering, the operation of removing the non-uniform background can cause distortion of sites, so that accuracy of resolution evaluation is affected.
On the one hand, the resolution evaluation method provided by the embodiment of the invention has the advantages that the area of the "+" pattern is smaller (35 multiplied by 35 mu m 2), the background is more uniform in a small area, and compared with the traditional method, the situation of uneven background is avoided. On the other hand, the invention directly performs fast Fourier transform on the image to obtain a corresponding frequency domain signal, as shown in fig. 3d and 3f, a low frequency signal close to 0 on the left side of the 1 st frequency spectrum peak, namely a frequency spectrum of an uneven background. The low frequency signal can be clearly distinguished from the 1 st to 24 th spectral peaks corresponding to the "+" pattern of the spatial domain, so that from the frequency domain perspective, it is not necessary to remove the non-uniform background before the resolution evaluation. Compared with the traditional method, the resolution evaluation method provided by the embodiment of the invention increases the robustness of resolution evaluation.
The embodiment of the invention provides a resolution evaluation method, which is used for collecting images to be analyzed of a resolution plate; calculating an intensity function of the image to be analyzed; performing fast Fourier transform according to the intensity function to obtain a target frequency spectrum of the image to be analyzed; determining the number of target spectrum peaks contained in the target spectrum; traversing a preset mapping table according to the number of the target spectrum peaks to obtain a resolution value of the optical imaging system. By using the embodiment of the invention, the number of spectrum peaks in the frequency domain can be counted by a method of performing fast Fourier transform on the spatial domain, so that the resolution evaluation capability can be improved.
The foregoing is a detailed description of the methods provided by embodiments of the present invention. The order of execution of the blocks in the flowchart illustrated may be changed, and some blocks may be omitted, depending on the particular needs. The gene sequencer 1 according to the embodiment of the present invention will be described below.
The embodiment of the invention also provides a gene sequencer, which comprises a memory, a processor and a computer program stored in the memory and capable of running on the processor, wherein the processor realizes the steps of the resolution evaluation method in any one of the embodiments when executing the program. It should be noted that the gene sequencer may include a chip platform, an optical system, and a liquid path system. Wherein, the chip platform can be used for loading the biochip, the optical system can be used for acquiring fluorescent images, and the liquid path system can be used for carrying out biochemical reaction by using preset reagents.
FIG. 5 is a schematic diagram showing the structure of a gene sequencer according to an embodiment of the present invention. As shown in fig. 5, the gene sequencer 1 includes a memory 10, and the gene sequencing system 100 is stored in the memory 10. The gene sequencing system 100 may acquire images to be analyzed of the resolution plate; calculating an intensity function of the image to be analyzed; performing fast Fourier transform according to the intensity function to obtain a target frequency spectrum of the image to be analyzed; determining the number of target spectrum peaks contained in the target spectrum; traversing a preset mapping table according to the number of the target spectrum peaks to obtain a resolution value of the optical imaging system. By using the embodiment of the invention, the number of spectrum peaks in the frequency domain can be counted by a method of performing fast Fourier transform on the spatial domain, so that the resolution evaluation capability can be improved.
In this embodiment, the gene sequencer 1 may further include a display 20 and a processor 30. The memory 10 and the display 20 may be electrically connected to the processor 30, respectively.
The memory 10 may be a different type of storage device for storing various types of data. For example, the memory and the memory of the gene sequencer 1 may be used, and the memory card may be a flash memory, an SM card (SMART MEDIA CARD ), an SD card (Secure DIGITAL CARD, secure digital card) or the like, which can be externally connected to the gene sequencer 1. In addition, memory 10 may include non-volatile memory, such as a hard disk, memory, a plug-in hard disk, a smart memory card (SMART MEDIA CARD, SMC), a Secure Digital (SD) card, a flash memory card (FLASH CARD), at least one disk storage device, a flash memory device, or other non-volatile solid-state storage device. The memory 10 is used for storing various kinds of data, such as various kinds of application programs (Applications) installed in the gene sequencer 1, data set and acquired by applying the above-described resolution evaluation method, and the like.
The display 20 is mounted on the gene sequencer 1 for displaying information.
The processor 30 is used for executing the resolution evaluation method and various software installed in the gene sequencer 1, such as an operating system and application display software. The processor 30 includes, but is not limited to, a processor (Central Processing Unit, CPU), a micro-control unit (Micro Controller Unit, MCU), etc. for interpreting computer instructions and processing data in computer software.
The gene sequencing system 100 may include one or more modules that are stored in the memory 10 of the gene sequencer 1 and configured to be executed by one or more processors (one processor 30 in this embodiment) to complete the embodiments of the present invention.
Referring to fig. 6, when the gene sequencing system 100 is used for performing image sharpness analysis on fluorescent images, the gene sequencing system 100 may include an image acquisition module 101, a function calculation module 102, a spectrum acquisition module 103, a quantity determination module 104, and a resolution determination module 105. Modules referred to in the embodiments of the present invention may be program segments, which perform a particular function and are more suited to describing software execution within the processor 30 than programs.
It will be appreciated that, corresponding to each of the embodiments of the resolution assessment method described above, the genetic sequencing system 100 may include some or all of the functional modules shown in FIG. 6, the function of each module being described in more detail below. It should be noted that the same terms and related terms and their specific explanations in the embodiments of the above resolution evaluation method may also be applied to the following functional descriptions of the modules. For the sake of space saving and repetition avoidance, the description is omitted.
The image acquisition module 101 may be used to acquire an image to be analyzed of the resolution plate.
The function calculation module 102 may be configured to calculate an intensity function of the image to be analyzed.
The spectrum acquisition module 103 may be configured to perform a fast fourier transform according to the intensity function, so as to obtain a target spectrum of the image to be analyzed.
The number determination module 104 may be configured to determine a number of target spectral peaks contained in the target spectrum.
The resolution determining module 105 may be configured to traverse a preset mapping table according to the target number of spectral peaks to obtain a resolution value of the optical imaging system.
The embodiment of the present invention also provides a computer-readable storage medium having stored thereon a computer program which, when executed by the processor 30, implements the steps of the resolution evaluation method in any of the above embodiments.
The modules/units of the gene sequencing system 100/gene sequencer integration, if implemented in the form of software functional units and sold or used as stand-alone products, may be stored in a computer readable storage medium. Based on such understanding, the present invention may implement all or part of the flow of the method of the foregoing embodiment, or may be implemented by a computer program to instruct related hardware, where the computer program may be stored in a computer readable storage medium, and the computer program may implement the steps of each of the foregoing method embodiments when executed by the processor 30. Wherein the computer program comprises computer program code which may be in source code form, object code form, executable file or some intermediate form etc. The computer readable storage medium may include: any entity or device capable of carrying the computer program code, a recording medium, a U disk, a removable hard disk, a magnetic disk, an optical disk, a computer Memory, a Read-Only Memory (ROM), or the like.
The Processor 30 may be a central processing unit (Central Processing Unit, CPU), other general purpose Processor, digital signal Processor (DIGITAL SIGNAL Processor, DSP), application SPECIFIC INTEGRATED Circuit (ASIC), field-Programmable gate array (Field-Programmable GATE ARRAY, FPGA) or other Programmable logic device, discrete gate or transistor logic device, discrete hardware components, or the like. The general purpose processor may be a microprocessor or the processor may be any conventional processor or the like, and the processor 30 is a control center of the gene sequencing system 100/gene sequencer 1, and connects the various parts of the whole gene sequencing system 100/gene sequencer 1 using various interfaces and lines.
The memory 10 is used for storing the computer program and/or the module, and the processor 30 implements various functions of the gene sequencing system 100/gene sequencer 1 by running or executing the computer program and/or the module stored in the memory 10 and calling the data stored in the memory 10. The memory 10 may mainly include a storage program area and a storage data area, wherein the storage program area may store an operating system, an application program (such as a sound playing function, an image playing function, etc.) required for at least one function, and the like; the storage data area may store data created according to the use of the gene sequencer 1, or the like.
In the several embodiments provided herein, it should be understood that the disclosed gene sequencer and method may be implemented in other ways. For example, the system embodiments described above are merely illustrative, e.g., the division of the modules is merely a logical function division, and other manners of division may be implemented in practice.
It will be evident to those skilled in the art that the embodiments of the invention are not limited to the details of the foregoing illustrative embodiments, and that the embodiments of the present invention may be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The present embodiments are, therefore, to be considered in all respects as illustrative and not restrictive, the scope of embodiments being indicated by the appended claims rather than by the foregoing description, and all changes which come within the meaning and range of equivalency of the claims are therefore intended to be embraced therein. Any reference sign in a claim should not be construed as limiting the claim concerned. A plurality of units, modules or means recited in the system, means or gene sequencer claims may also be implemented by the same unit, module or means in software or hardware.
The foregoing embodiments are merely for illustrating the technical solution of the embodiment of the present invention, but not for limiting the same, although the embodiment of the present invention has been described in detail with reference to the foregoing preferred embodiments, it will be understood by those skilled in the art that modifications and equivalent substitutions may be made to the technical solution of the embodiment of the present invention without departing from the spirit and scope of the technical solution of the embodiment of the present invention.

Claims (5)

1. A resolution plate for detecting resolution of an optical imaging system in gene sequencing, the resolution plate comprising: the resolution test image is formed by a plurality of sites which are in central symmetry, the sites are in central symmetry patterns, and the distances between adjacent sites in the same direction are gradually increased from the central point to the outside in an equi-differential sequence.
2. A method for resolution evaluation using the resolution plate of claim 1, applied to an optical imaging system, wherein the resolution evaluation method comprises:
Collecting an image to be analyzed of the resolution plate;
calculating an intensity function of the image to be analyzed, wherein the intensity function is the relation between the position information of the pixel points in the image to be analyzed and the brightness value corresponding to the pixel points;
Performing fast fourier transform according to the intensity function to obtain a target spectrum of the image to be analyzed, including: acquiring a first image of the image to be analyzed along a preset direction; when the number of the preset directions is greater than 1, respectively acquiring a first image set of the image to be analyzed along the preset directions; calculating a one-dimensional intensity function of each image in the first image set to obtain a one-dimensional intensity function set; calculating an average value according to each one-dimensional intensity function in the one-dimensional intensity function set to obtain a one-dimensional average intensity function; performing one-dimensional fast Fourier transform according to the one-dimensional average intensity function to obtain a first target frequency spectrum of the first image set; or calculating a two-dimensional intensity function of the image to be analyzed; performing two-dimensional fast Fourier transform according to the two-dimensional intensity function to obtain a second target frequency spectrum of the image to be analyzed; the target spectrum comprises a resolvable region and an unresolved region;
Determining a target number of spectral peaks contained in the target spectrum, comprising: acquiring the resolvable region corresponding to the target frequency spectrum; calculating a maximum value of the number of spectral peaks contained in the distinguishable region; determining the maximum value as a target spectrum peak number;
Traversing a preset mapping table according to the number of the target spectrum peaks to obtain a resolution value of the optical imaging system.
3. A gene sequencing system for performing the resolution assessment method of claim 2, wherein the gene sequencing system comprises:
the image acquisition module is used for acquiring an image to be analyzed of the resolution board;
The function calculation module is used for calculating the intensity function of the image to be analyzed;
The spectrum acquisition module is used for executing fast Fourier transform according to the intensity function to obtain a target spectrum of the image to be analyzed, and comprises the following steps: acquiring a first image of the image to be analyzed along a preset direction; when the number of the preset directions is greater than 1, respectively acquiring a first image set of the image to be analyzed along the preset directions; calculating a one-dimensional intensity function of each image in the first image set to obtain a one-dimensional intensity function set; calculating an average value according to each one-dimensional intensity function in the one-dimensional intensity function set to obtain a one-dimensional average intensity function; performing one-dimensional fast Fourier transform according to the one-dimensional average intensity function to obtain a first target frequency spectrum of the first image set; or calculating a two-dimensional intensity function of the image to be analyzed; performing two-dimensional fast Fourier transform according to the two-dimensional intensity function to obtain a second target frequency spectrum of the image to be analyzed; the target spectrum comprises a resolvable region and an unresolved region;
The number determining module is configured to determine a number of target spectrum peaks included in the target spectrum, and includes: acquiring the resolvable region corresponding to the target frequency spectrum; calculating a maximum value of the number of spectral peaks contained in the distinguishable region; determining the maximum value as a target spectrum peak number;
And the resolution determining module is used for traversing a preset mapping table according to the number of the target spectrum peaks to obtain a resolution value of the optical imaging system.
4. A gene sequencer, characterized in that it comprises a processor for implementing the steps of the resolution assessment method according to claim 2 when executing a computer program stored in a memory.
5. A computer-readable storage medium, on which a computer program is stored, characterized in that the computer program, when being executed by a processor, implements the steps of the resolution evaluation method according to claim 2.
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