Resolution board, resolution evaluation method and related equipment
阅读说明：本技术 分辨率板、分辨率评估方法及相关设备 (Resolution board, resolution evaluation method and related equipment ) 是由 伯恩 徐洪 于 2020-05-13 设计创作，主要内容包括：本发明提供一种分辨率板,包括：基板以及在所述基板上设置的分辨率测试图像,所述分辨率测试图像由呈中心对称的若干位点组成,同一方向上相邻所述位点的间距从中心点向外逐渐变大。本发明还提供一种利用所述分辨率板进行分辨率评估的方法、基因测序系统、基因测序仪及计算机可读存储介质。利用本发明实施例,能够提高分辨率评估的效率与鲁棒性。(The present invention provides a resolution board comprising: the resolution test image is composed of a plurality of centrosymmetric sites, and the distance between every two adjacent sites in the same direction is gradually increased from the central 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 robustness of resolution evaluation can be improved.)
1. A resolution board, characterized in that the resolution board comprises: the resolution test image is composed of a plurality of centrosymmetric sites, and the distance between every two adjacent sites in the same direction is gradually increased from the central point to the outside.
2. The resolution board according to claim 1, wherein 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 to the outside.
3. A method for evaluating resolution using the resolution board according to any one of claims 1 to 2, applied to an optical imaging system, wherein the resolution evaluating method comprises:
collecting an image to be analyzed of the resolution board;
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;
and 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. The resolution evaluation method according to claim 3, wherein the performing a fast Fourier transform according to the intensity function to obtain a target spectrum of the image to be analyzed comprises:
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.
5. The resolution evaluation method according to claim 4, further comprising:
when the number of the preset directions is more 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.
6. The resolution evaluation method according to claim 3, wherein the performing a fast Fourier transform according to the intensity function to obtain a target spectrum of the image to be analyzed further comprises:
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.
7. The method of claim 3, wherein the determining the number of target spectral peaks included in the target spectrum comprises:
acquiring a distinguishable region corresponding to the target frequency spectrum;
calculating the maximum value of the number of spectrum peaks contained in the distinguishable region;
and determining the maximum value as the number of target spectrum peaks.
8. A gene sequencing system, comprising:
the image acquisition module is used for acquiring an image to be analyzed of the resolution plate;
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.
9. A gene sequencer comprising a processor for implementing the steps of the resolution assessment method of any one of claims 3 to 7 when executing a computer program stored in a memory.
10. A computer-readable storage medium, on which a computer program is stored, which, when being executed by a processor, carries out the steps of the resolution evaluation method according to one of claims 3 to 7.
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 is the 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 commonly used at present is: the four bases carry different fluorophores respectively, the different fluorophores emit fluorescence with different wavelengths (colors) after being excited, and the types of the synthesized bases can be identified by identifying the fluorescence wavelengths, so that the base sequences can be read. The second generation sequencing technology adopts a high resolution microscopic imaging system, takes pictures to collect fluorescent molecular images of DNA nanospheres (DNB, DNAnnoballs) on a biochip (gene sequencing chip), and sends the fluorescent molecular images into base recognition software to decipher image signals to obtain a base sequence. The imaging quality of the gene sequencer microscopic imaging link has a great influence on the accuracy of base identification, and the imaging quality is directly influenced by the quality of the resolution of a microscopic imaging system.
In the prior art, a 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 judging whether the adjacent line intensity values of an observation line pair can be separated; the ESF/MTF method determines the resolution of the imaging system by calculating the ESF (edge spread Function) and MTF (modulation Transfer Function) of the diagonal trapezoid. However, neither of the above two methods can directly evaluate whether the adjacent DNA nanospheres are distinguishable, and the two methods are greatly influenced by environmental factors, resulting in low efficiency of resolution evaluation.
Disclosure of Invention
In view of the above, there is a need for a resolution board, a resolution evaluation method, a gene sequencing system, a gene sequencer and a storage medium, which can improve the efficiency and robustness of resolution evaluation for the 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 board, including: the resolution test image is composed of a plurality of centrosymmetric sites, and the distance between every two adjacent sites in the same direction is gradually increased from the central point to the outside.
Further, in the resolution board provided in the embodiment of the present invention, the position points are centrosymmetric patterns, and the distances between adjacent position points in the same direction are increased in an arithmetic progression from the central point to the outside.
The second aspect of the embodiments of the present invention further provides a method for evaluating resolution by using the resolution plate described in any one of the above, where the method is applied to an optical imaging system, and the method for evaluating resolution includes:
collecting an image to be analyzed of the resolution board;
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;
and 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 resolution evaluation method provided in an embodiment of the present invention, the performing fast fourier transform according to the intensity function to obtain a 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 foregoing resolution evaluation method provided in an embodiment of the present invention, the method further includes:
when the number of the preset directions is more 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 resolution evaluation method provided in an embodiment of the present invention, the performing fast fourier transform according to the intensity function to obtain a 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 evaluating method provided in an embodiment of the present invention, the determining the number of target spectrum peaks included in the target spectrum includes:
acquiring a distinguishable region corresponding to the target frequency spectrum;
calculating the maximum value of the number of spectrum peaks contained in the distinguishable region;
and determining the maximum value as the number of target spectrum peaks.
The third aspect of the embodiments of the present invention also provides a gene sequencing system, including:
the image acquisition module is used for acquiring an image to be analyzed of the resolution plate;
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.
The fourth aspect of the embodiments of the present invention further provides a gene sequencer, which includes a processor, and the processor is configured to implement the steps of the resolution evaluation method according to any one of the above items when executing the computer program stored in the memory.
The fifth aspect of the embodiments of the present invention also provides a computer-readable storage medium, on which a computer program is stored, where the computer program, when executed by a processor, implements the steps of the resolution evaluation method described in any one of the above.
The embodiment of the invention provides a resolution plate, a resolution evaluation method, a gene sequencing system, a gene sequencer and a computer readable storage medium, aiming at the conditions of small molecular size and small space of DNA nanospheres and/or biological macromolecules and the like, the resolution plate with the space between adjacent sites gradually increased from a central point to the outside is designed, the resolution is determined by evaluating the minimum space which can be resolved by an optical imaging system, and the efficiency and robustness of resolution evaluation can be improved. In addition, the invention can improve the resolution evaluation capability by counting the number of spectral peaks in the frequency domain by a method of performing fast Fourier transform on the spatial domain.
Drawings
Fig. 1 is a schematic diagram of a resolution board 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 board according to an embodiment of the 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 the spatial domain according to an embodiment of the present invention.
Fig. 3d is a one-dimensional fourier spectrum diagram of the intensity function of fig. 3c in the frequency domain.
Fig. 3e is a schematic diagram of the two-dimensional fourier spectrum corresponding to fig. 3 b.
Fig. 3f is a one-dimensional spectrum diagram of the dashed box portion of 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 structural diagram of a gene sequencer according to an embodiment of the present invention.
FIG. 6 is a functional block diagram of an exemplary gene sequencer shown in FIG. 5.
The following detailed description will further illustrate the invention in conjunction with the above-described figures.
Detailed Description
In order that the above objects, features and advantages of the present invention can be more clearly understood, a detailed description of the present invention will be given below with reference to the accompanying drawings and specific embodiments. It should be noted that the embodiments and features of the embodiments of the present application may be combined with each other without conflict.
In the following description, numerous specific details are set forth to provide a thorough understanding of the present invention, and the described embodiments are a part, but not all, of the present invention. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present 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 in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention.
Referring to fig. 1, (a), (b), (c), (d), (e), (f), (g), (h) and (i) in fig. 1 are schematic diagrams of a resolution board according to an embodiment of the present invention. The resolution plate can be designed aiming at the characteristics that the molecular size of biomacromolecules in molecular fluorescence detection and/or DNA nanospheres in a gene sequencer is small and the biomacromolecules and/or the DNA nanospheres are regularly arranged, 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 can detect and image single or multiple molecules in a medium such as a solution, so that the chemical reaction pathway can be monitored in real time, and particularly, biological macromolecules are detected and information between molecular structures and functions is provided, including gene sequencing analysis.
As shown in fig. 1, the resolution board includes: the resolution test image (an image formed by white points of each figure in figure 1 is a resolution test image) is formed by a plurality of centrosymmetric points, and the distance between every two adjacent points in the same direction is gradually increased from the central point to the outside. Wherein the resolution test image may be a dot column pattern. The boundaries of the resolution test image are not limited (the peripheral frame of each image in fig. 1 is only 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 centrosymmetric sites, on one hand, the centrosymmetric pattern can contain the same number of points on four branches, and the total number of points is the largest, so that the number of 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 centrosymmetric, the pattern can only obtain more points in a few directions, and meanwhile, the number of points on some branches is too small, and the branches cannot be used for subsequent algorithms); on the other hand, the optical imaging system has the best imaging quality at the center of the field of view, so that the center of the resolution test image is positioned at the center of the field of view, and the center of the field of view is used for imaging denser points.
In an embodiment of the present invention, the position points are in a central symmetrical pattern, for example, the position points may be one of a circle, a square, a regular triangle, a regular hexagon, and a regular octagon. The sites extend outward from a central point along a horizontal direction and/or a vertical direction. The distance between the adjacent sites in the same direction is increased outwards from the central point in an arithmetic progression. The material of the substrate may include: optical glass, fused silica, optical ceramic material and silicon wafer.
In at least one embodiment of the present invention, the maximum point numbers M and N of the central point (including the central point) of the resolution test image outward in the horizontal direction and/or the vertical direction are respectively obtained.Andthe distances between adjacent points in the horizontal direction and the vertical direction from the center point of the resolution test image, respectively, where nxAnd nyAre all integers, and nx∈[1,M-1],ny∈[1,N-1]。
In at least one embodiment of the present invention, in designing the resolution plate, it is assumed that the resolutions of the optical imaging system in the x and y directions are R, respectivelyxAnd RySpacing of adjacent said sitesAndare arranged in an arithmetic progression. It is understood that when the above-mentioned material is used, the above-mentioned material can beAnd/orThe two points are not distinguishable by the optical imaging system. That is, the resolution of the optical imaging system can be evaluated by determining which two adjacent sites cannot be separated by the optical imaging system.
An embodiment of the present invention provides a resolution board, including: the resolution test image is composed of a plurality of centrosymmetric sites, and the distance between every two adjacent sites in the same direction is gradually increased from the central point to the outside. The invention designs a resolution ratio plate aiming at the characteristics that the molecular size of the DNA nanospheres and the like in a biomacromolecule and/or gene sequencer in molecular fluorescence detection is small and the DNA nanospheres and the like are regularly arranged, well simulates the ideal environment of an optical imaging system based on the biomacromolecule or the DNA nanospheres, and thus, the resolution ratio can be effectively evaluated.
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 evaluating the resolution by utilizing the resolution plate, and the resolution evaluation method can be used in an optical imaging system. As shown in fig. 2, the resolution evaluation method may include the steps of:
and 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 positions are circular, the diameter d is 500nm, M is 28, the resolution test image is a resolution plate of a "+" pattern of (g) in fig. 1, and an optical imaging system is called to acquire the resolution plate to obtain an image to be analyzed of the resolution plate, as shown in fig. 3b, and fig. 3b is a schematic diagram of the resolution plate image acquired by the optical imaging system according to an embodiment of the present invention.
And S22, calculating the intensity function of the image to be analyzed.
In at least one embodiment of the present invention, the intensity function is a relation function between position information of a pixel point in the image to be analyzed and a corresponding brightness value of the pixel point. The pixel point can be understood as a minimum image unit recognizable by an 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 the corresponding brightness value of the pixel point; and determining a functional relation between the position information and the brightness value, wherein the functional relation is an 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), wherein y0Is a constant and can be set according to actual requirements; the second mentionedThe dimensional intensity function is denoted as f (x, y).
And S23, performing fast Fourier transform according to the intensity function to obtain the target frequency spectrum of the image to be analyzed.
In at least one embodiment of the present invention, the spacing for adjacent sites in the spatial domain in the horizontal and vertical directionsAndthe frequency spectrum peak is a point array which is arranged in an arithmetic progression, the distance between adjacent points is equivalent to the period of a signal, and the distance values are different, so that the corresponding frequencies in the frequency domain are different, a plurality of frequency spectrum peaks which are different in frequency and sparse are formed, and two dense adjacent points in the spatial domain are easier to distinguish in the frequency spectrum domain. And the spacing of adjacent sites in the spatial domainAndthe number of the frequency peaks is consistent with the number of the frequency peaks in the frequency domain, so that the number of the frequency peaks is counted to judge which two adjacent sites in the spatial domain can be distinguished, 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 may be one-to-one corresponding to the number of different spacings of adjacent sites in the spatial domain by space-frequency conversion (i.e., fast fourier transform). The fast Fourier transform comprises one-dimensional fast Fourier transform and 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 frequency 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 the preset direction may be 1 direction or multiple directions, which is not limited herein. Said performing a one-dimensional fast Fourier transform according to said one-dimensional intensity function comprises: inputting the one-dimensional intensity function into equation (1):
wherein, F1D(u) represents a one-dimensional fourier transform of f (x), f (x) is a one-dimensional intensity function along the x direction, 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 one embodiment, f (x) is f (x, y)0) Abbreviation of (a), y0Q/2 (representing selecting a line of intensity values in the middle of the y axis), where Q is the number of pixels in the y direction of the image to be analyzed.
Illustratively, for a resolution board whose resolution test image is a "+" pattern of fig. 1 (g), one branch along the x or y direction corresponds to the first image, as shown by the dashed box in fig. 3 b. As shown in fig. 3c, fig. 3c is a schematic diagram of an intensity function in a spatial domain according to an embodiment of the present invention. Performing a one-dimensional fast fourier transform according to the one-dimensional intensity function to obtain a first target spectrum of the first intensity image, as shown in fig. 3d, where fig. 3d is a one-dimensional fourier spectrum diagram of the intensity function of fig. 3c in a frequency domain.
Observing fig. 3c, it can be seen that in the spatial domain, the arrangement of peaks (from left to right) gradually becomes dense from sparse, and adjacent peaks are overlapped to form peaks with higher amplitude and narrower width. When adjacent peaks are dense to some extent, the peaks formed by the superposition become less distinct (but still present), leading to inaccuracies in the resolution assessment. In FIG. 3c, there are 22 peaks from left to right (the number of peaks in the spatial domain can be numberedMarks), correspondingTherefore, the resolution value of the optical imaging system in the x direction is obtained by directly counting the peaks in the spatial domain and traversing the preset mapping table according to the number of the peaks in the spatial domain, and is 750. The preset mapping table is a factory preset value, and as shown in fig. 4, the preset mapping table includes mapping relationships among spatial domain point sequence numbers, spatial domain adjacent site distances, spectral peak numbers, and optical imaging system resolutions.
Observing fig. 3d, it can be seen that there are 24 significant spectral peaks in the frequency domain from left to right (low to high frequencies). The spectral peaks correspond to different frequencies, the different frequencies correspond to different periods, and the different periods correspond to different adjacent dot spacings in the spatial domain, wherein the low-frequency spectral peaks correspond to a larger adjacent dot spacing and the high-frequency spectral peaks correspond to a smaller adjacent dot spacing. Because there are 24 frequency spectrum peaks from low to high (the number of peaks in frequency domain can be marked by numbers), the corresponding adjacent point interval isTherefore, the peak in the frequency domain is directly counted, and the resolution value of the optical imaging system in the x direction is obtained by traversing the preset mapping table according to the number of the peaks in the frequency domain, namely 650 nm.
Therefore, by adopting the resolution evaluation method provided by the embodiment of the invention, the method of performing fast Fourier transform on the spatial domain counts the number of spectral peaks in the frequency domain, and the resolution evaluation capability can be improved.
In at least one embodiment of the present invention, because the quality of the resolution board may cause a "defect" phenomenon in the image to be analyzed, for such a problem, the intensity values of the plurality of branches may be selected to be weighted and averaged first, and then one-dimensional fourier transform is performed. Specifically, the method further comprises: when the number of the preset directions is more 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 frequency 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 require the selection of different branches of the resolution board, but directly performs the two-dimensional fast fourier transform on the two-dimensional intensity function of the resolution board. Specifically, the performing of the two-dimensional fast fourier transform according to the two-dimensional intensity function includes: inputting the two-dimensional intensity function to equation (2):
wherein, F2D(u, v) represents a 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.
Illustratively, for the resolution test image of the resolution board with a "+" pattern as shown in fig. 1 (g), as shown in fig. 3e, fig. 3e is a schematic diagram of the corresponding two-dimensional fourier spectrum of fig. 3b, and the two-dimensional fourier spectrum is in a "+" pattern. Here, to show the spectral details, a branch of the two-dimensional Fourier spectrogram along the x-direction (as shown by the dashed box in FIG. 3 e) is taken, and the spectral amplitude is represented as shown in FIG. 3f, which is the dashed box in FIG. 3eA one-dimensional spectral diagram. As shown in FIG. 3f, there are 24 peaks in the spectrum from left to right (low to high frequency), soThe resolution in the x-direction of the optical imaging system is 650 nm. 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 also be determined by counting the number of spectral peaks.
It will be appreciated that the benefit of using a two-dimensional fourier transform directly against the resolution plate is that the accuracy of the determination can be achieved by counting the number of spectral peaks in the frequency domain, without being affected by the "defect" phenomenon of the resolution plate.
And 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 a non-resolvable region, and a spectrum peak of the resolvable region is referred to as a target spectrum peak. As shown in fig. 3d, there are higher frequency spectrum peaks at the right side of the 24 th spectrum peak, but since the peak values are smaller and clutter interference exists, it is indicated that there is an interference signal in the spatial domain and the distance between the adjacent sites is the same, and thus it is determined as an unresolvable 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 indistinguishable region.
The determining the number of target spectrum peaks included in the target spectrum comprises: acquiring a distinguishable region corresponding to the target frequency spectrum; calculating the maximum value of the number of spectrum peaks contained in the distinguishable region; and determining the maximum value as the number of target spectrum peaks. Wherein, the calculating the maximum value of the number of the spectral peaks contained in the distinguishable region can adopt a direct observation spectrogram and count the smoother (without clutter interference) spectral peaks; or the number of the spectrum peaks can be counted by adopting a machine learning method and the like.
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 spectrum 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 between adjacent space points in a space domain, the number of frequency spectrum peaks and the resolution of the optical imaging system. The space between the space domain point serial number and the space domain adjacent site is known in advance, and the number of the frequency spectrum peaks and the resolution of the optical imaging system can be obtained through multiple calculations. It can be understood that the resolution of the optical imaging system is evaluated by traversing the preset mapping table, so that the evaluation efficiency of the resolution can be improved.
It can be understood that, when the resolution is evaluated, the image to be analyzed needs to be preprocessed, for example, to remove an uneven background, etc., because the area of the image to be analyzed for evaluating the resolution is large. The acquisition of the uneven background is mainly realized through low-pass filtering, on one hand, parameters of the low-pass filtering need to be adjusted repeatedly according to illumination conditions, and on the other hand, the uneven background is difficult to obtain perfectly through adjustment of the parameters of the low-pass filtering, so that the operation of removing the uneven background can cause distortion of a locus, and the accuracy of resolution evaluation is influenced.
On the other hand, the resolution evaluation method provided by the embodiment of the invention has the advantage that the area of the '+' pattern is small (-35 x 35 μm)2) The background is relatively uniform in a small area, and compared with the traditional method, the situation of non-uniform background does not exist. On the other hand, the invention directly performs fast fourier transform on the image to obtain the corresponding frequency domain signal, as shown in fig. 3d and fig. 3f, the low frequency signal close to 0 on the left side of the 1 st spectral peak, i.e. the spectrum of the uneven background, is obtained. The low frequency signal is clearly distinguishable from the 1 st to 24 th spectral peaks corresponding to the "+" pattern in the spatial domain, so that from the frequency domain perspective, it is not necessary to remove the uneven background prior to resolution evaluation. Compared with the traditional method, the resolution evaluation method provided by the embodiment of the invention has the advantage that the robustness of resolution evaluation is improved.
The embodiment of the invention provides a resolution evaluation method, which comprises the steps of collecting an image 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; and 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 utilizing the embodiment of the invention, the number of the frequency spectrum peaks in the frequency domain is counted by a method of performing fast Fourier transform on the spatial domain, so that the resolution evaluation capability can be improved.
The above is a detailed description of the method provided by the embodiments of the present invention. The order of execution of the blocks in the flowcharts shown may be changed, and some blocks may be omitted, according to various needs. The gene sequencer 1 provided in 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 which is stored on the memory and can be run on the processor, wherein the processor executes the program to realize the steps of the resolution evaluation method in any one of the above embodiments. The gene sequencer may include a chip platform, an optical system, and a liquid path system. The chip platform can be used for loading a biochip, the optical system can be used for acquiring a fluorescence image, and the liquid path system can be used for carrying out biochemical reaction by utilizing a preset reagent.
FIG. 5 is a schematic structural diagram 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 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; and 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 utilizing the embodiment of the invention, the number of the frequency spectrum peaks in the frequency domain is 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 screen 20 can be electrically connected with the processor 30 respectively.
The memory 10 may be of different types of memory devices for storing various types of data. For example, the memory or internal memory of the gene sequencer 1 may be used, and a memory Card such as a flash memory, an SM Card (Smart Media Card), an SD Card (Secure Digital Card), or the like may be externally connected to the gene sequencer 1. Further, the memory 10 may include a non-volatile memory, such as a hard disk, a memory, a plug-in hard disk, a Smart Media Card (SMC), a Secure Digital (SD) Card, a Flash memory Card (Flash Card), at least one magnetic disk storage device, a Flash memory device, or other non-volatile solid state storage device. The memory 10 is used for storing various types of data, for example, various types 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 screen 20 is installed on the gene sequencer 1 and is used for displaying information.
The processor 30 is used for executing the resolution evaluation method and various types of 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 Central Processing Unit (CPU), a Micro Controller Unit (MCU), and other devices for interpreting computer instructions and Processing data in computer software.
The gene sequencing system 100 may include one or more modules stored in the memory 10 of the gene sequencer 1 and configured to be executed by one or more processors (in this embodiment, one processor 30) to accomplish embodiments of the present invention.
Referring to fig. 6, when the gene sequencing system 100 is used for image sharpness analysis of a fluorescence image, 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. The modules referred to in the embodiments of the present invention may be program segments that perform a specific function, and are more suitable than programs for describing the execution process of software in the processor 30.
It is understood that, in correspondence with each embodiment of the above-described resolution evaluation method, the gene sequencing system 100 may include some or all of the functional modules shown in fig. 6, and the functions of the modules will be described in detail below. It should be noted that the same terms, related terms, and specific explanations thereof in the above embodiments of the resolution evaluation method can also be applied to the following functional descriptions of the modules. For brevity and to avoid repetition, further description is omitted.
The image acquisition module 101 may be used to acquire an image to be analyzed of the resolution plate.
The function computation module 102 may be configured to compute an intensity function of the image to be analyzed.
The spectrum obtaining module 103 may be configured to perform fast fourier transform according to the intensity function 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 comprised by the target spectrum.
The resolution determination module 105 may be configured to traverse a preset mapping table according to the number of target spectral peaks to obtain a resolution value of the optical imaging system.
The embodiment of the present invention further provides a computer-readable storage medium, on which a computer program is stored, and the computer program, when executed by the processor 30, implements the steps of the resolution evaluation method in any of the above embodiments.
The gene sequencing system 100/gene sequencer integrated module/unit, if implemented as a software functional unit and sold or used as a stand-alone product, may be stored in a computer readable storage medium. Based on such understanding, all or part of the flow in the method according to the above embodiments may be implemented by a computer program, which may be stored in a computer readable storage medium and used by the processor 30 to implement the steps of the above method embodiments. Wherein the computer program comprises computer program code, which may be in the form of source code, object code, an 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, recording medium, U disk, removable hard disk, magnetic disk, optical disk, computer Memory, Read-Only Memory (ROM), or the like.
The Processor 30 may be a Central Processing Unit (CPU), other general purpose Processor, a Digital Signal Processor (DSP), an Application Specific Integrated Circuit (ASIC), a Field Programmable Gate Array (FPGA) or other Programmable logic device, discrete Gate or transistor logic device, discrete hardware component, or the like. The general purpose processor may be a microprocessor or the processor may be any conventional processor, etc., and the processor 30 is a control center of the gene sequencing system 100/gene sequencer 1, and various interfaces and lines are used to connect the various parts of the whole gene sequencing system 100/gene sequencer 1.
The memory 10 is used for storing the computer programs and/or modules, and the processor 30 implements various functions of the gene sequencing system 100/gene sequencer 1 by running or executing the computer programs and/or modules 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 required by at least one function (such as a sound playing function, an image playing function, etc.), and the like; the storage data region may store data created according to the use of the gene sequencer 1, and the like.
In 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, and for example, the division of the modules is only one logical functional division, and other divisions may be realized in practice.
It will be evident to those skilled in the art that the embodiments of the present invention are not limited to the details of the foregoing illustrative embodiments, and that the embodiments of the present invention are capable of being embodied in other specific forms without departing from the spirit or essential attributes thereof. The present embodiments are therefore to be considered in all respects as illustrative and not restrictive, the scope of the 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. Several of the units, modules or devices recited in the system, device or gene sequencer claims may also be implemented by one and the same unit, module or device, either in software or hardware.
Although the embodiments of the present invention have been described in detail with reference to the preferred embodiments, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the spirit and scope of the embodiments of the present invention.