CN110889825A - Single molecule positioning device - Google Patents
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Abstract
The embodiment of the invention discloses a monomolecular positioning device, which comprises: the determining module is used for determining a brightness value matrix corresponding to each pixel point of a target picture, wherein the brightness value matrix is a matrix which takes the brightness value of the pixel point as a center and has pixel point brightness values with preset line number and preset column number; the obtaining module is used for obtaining a binarization matrix of the target picture according to the brightness value matrix; the determining module is further configured to determine a first connected component with a vertex value of 1 from the binarization matrix; and the calculation module is used for solving the central coordinate of the first connected component through a preset algorithm to serve as the two-dimensional position coordinate of the single molecule. Therefore, the embodiment of the invention can position single molecules.
Description
Technical Field
The invention relates to the technical field of computers, in particular to a monomolecular positioning device.
Background
In recent years, the super-resolution fluorescence imaging technology realizes observation of fine structures of living cells at a molecular level, becomes an extremely important tool for biological structure and functional imaging, and becomes an essential part of single-molecule sequencing technology. The super-resolution fluorescence imaging technology is a technology for visually displaying the spatial distribution of a single molecule with a spatial resolution of nanometer order. The super-resolution fluorescence imaging can be used for researching the interaction process between single molecules marked by fluorescent molecules and can be used for judging the extension condition of the base in the single molecule sequencing technology. The currently common super-resolution fluorescence imaging method is a microscopic imaging technology which utilizes the switching effect of fluorescent molecules to perform positioning. For example, light-sensitive positioning microscopy (PALM), random optical reconstruction microscopy (STORM), etc., which acquire the positioning information of sparsely distributed single molecules labeled by fluorescent molecules at different times, and then superimpose the positioning information acquired at different times to finally realize high transverse nanometer resolution. A super-resolution image is obtained by superposing a plurality of single molecule positions. Obviously, single molecule localization is an indispensable link in the super-resolution fluorescence imaging process. Therefore, it is important to provide a device capable of localizing single molecules.
Disclosure of Invention
The embodiment of the invention discloses a monomolecular positioning device which can position a monomolecular.
The embodiment of the invention discloses a monomolecular positioning device, which comprises:
the determining module is used for determining a brightness value matrix corresponding to each pixel point of a target picture, wherein the brightness value matrix is a matrix which takes the brightness value of the pixel point as a center and has pixel point brightness values with preset line number and preset column number;
the obtaining module is used for obtaining a binarization matrix of the target picture according to the brightness value matrix;
the determining module is further configured to determine a first connected component with a vertex value of 1 from the binarization matrix;
and the calculation module is used for solving the central coordinate of the first connected component through a preset algorithm to serve as the two-dimensional position coordinate of the single molecule.
In the embodiment of the invention, a determining module determines a brightness value matrix corresponding to each pixel point of a target picture, wherein the brightness value matrix is a matrix which takes the brightness value of the pixel point as a center and has pixel point brightness values with preset row number and preset column number; the obtaining module obtains a binarization matrix of the target picture according to the brightness value matrix, and the determining module determines a first connected component with a vertex value of 1 from the binarization matrix; and the calculation module calculates the center coordinate of the first connected component as the two-dimensional position coordinate of the single molecule through a preset algorithm. Therefore, the embodiment of the invention can position single molecules.
Drawings
In order to more clearly illustrate the technical solutions in the embodiments of the present invention, the drawings needed to be used in the embodiments will be briefly described below, and it is obvious that the drawings in the following description are some embodiments of the present invention, and it is obvious for those skilled in the art that other drawings can be obtained according to these drawings without creative efforts.
FIG. 1 is a schematic flow chart of a single molecule localization method according to an embodiment of the present invention;
FIG. 2 is a schematic flow chart of another single-molecule localization method disclosed in the embodiments of the present invention;
FIG. 3 is a schematic flow chart of another single-molecule localization method disclosed in the embodiments of the present invention;
FIG. 4 is a schematic structural diagram of a single-molecule positioning apparatus according to an embodiment of the present invention;
FIG. 5 is a schematic structural diagram of another single-molecule positioning device disclosed in the embodiments of the present invention;
FIG. 6 is a schematic structural diagram of another single-molecule positioning device disclosed in the embodiments of the present invention;
fig. 7 is a schematic diagram of pixel point distribution of a target picture according to an embodiment of the present invention.
Detailed Description
The technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the drawings in the embodiments of the present invention, and it is obvious that the described embodiments are some, not all, embodiments 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.
The embodiment of the invention discloses a monomolecular positioning method and a monomolecular positioning device, which can position a monomolecular. The following are detailed below.
Referring to fig. 1, fig. 1 is a schematic flow chart of a single-molecule positioning method according to an embodiment of the present invention. As shown in fig. 1, the single molecule localization method may include the following steps.
S101, aiming at each pixel point of a target picture, determining a brightness value matrix corresponding to the pixel point, wherein the brightness value matrix is a matrix which takes the brightness value of the pixel point as a center and has pixel point brightness values with preset line number and preset column number.
In the embodiment of the invention, a user can select or import a picture as a target picture in the single-molecule positioning device. The single molecule positioning device determines a brightness value matrix corresponding to each pixel point of the target picture. The luminance value matrix corresponding to the pixel point is a matrix taking the luminance value of the pixel point as the center, and the luminance value matrix corresponding to the pixel point is a matrix having pixel point luminance values with preset row numbers and preset column numbers. For example, the luminance value matrix corresponding to the pixel point may be a matrix of 3 × 3, 5 × 5, and 7 × 7 centered on the luminance value of the pixel point, which is not limited in the embodiment of the present invention. The single-molecule positioning device may include, but is not limited to, a smart phone, a tablet computer, a notebook computer, a desktop computer, and other user equipment. The operating system of the user equipment may include, but is not limited to, an Android operating system, an IOS operating system, a Symbian operating system, a Black Berry operating system, a Windows operating system, and the like, and the embodiment of the present invention is not limited thereto.
For example, when the target picture has 512 pixels, the single-molecule positioning device determines the brightness matrix corresponding to each pixel of the target picture, and the single-molecule positioning device will determine the total brightness matrix512 x 512 luminance value matrixes are determined. As shown in fig. 7, fig. 7 is a schematic diagram of pixel point distribution of a target picture, where n is 512, a11Is a pixel point of the first row and the first column, a12Is a pixel point of the first row and the second column, a1nIs the pixel point of the n-th column of the first row, …, annIs the pixel point of the nth row and the nth column. If the brightness value matrix is 3-by-3 matrix, the single molecule positioning device determines a11When the corresponding brightness value matrix is selected from the target picture, the value is selected as a11The central 3 x 3 pixel. In pixel point of target picture with a11The central 3 x 3 pixel point only comprises a12、a21And a22The single molecule positioning device will acquire a11、a12、a21And a22And a of the pixel points without the target picture11The brightness value of the pixel point of 3 x 3 as the center is set as 0; the single molecule positioning device will be represented by a11The brightness value of the central 3 x 3 pixel point constitutes a11A corresponding matrix of luminance values.
For example, if a11Corresponding brightness value of L11，a12Corresponding brightness value of L12，a21Corresponding brightness value of L21，a22Corresponding brightness value of L22Then is equal to a11Corresponding luminance value matrix A11Is composed of
In the same way as a12Corresponding luminance value matrix A12Is composed of
Wherein L is13Is a13Brightness value of L23Is a23The luminance value of (a). In the same way as a22Corresponding luminance value matrix A22Is composed of
Wherein L is31Is a31Brightness value of L32Is a32Brightness value of L33Is a33The luminance value of (a).
And S102, acquiring a binarization matrix of the target picture according to the brightness value matrix.
In the embodiment of the invention, after the single molecule positioning device determines the brightness value matrix corresponding to each pixel point, the binarization matrix of the target picture is obtained according to the determined brightness value matrix.
As an optional implementation manner, a specific implementation manner of the single molecule positioning apparatus obtaining the binarization matrix of the target picture according to the luminance value matrix may include the following steps:
11) calculating the similarity value of each brightness value matrix and a preset matrix by the monomolecular positioning device to obtain a similarity value matrix;
12) the single molecule positioning device compares each similarity value in the similarity value matrix with a preset threshold value to obtain a comparison result corresponding to each similarity value;
13) and the unimolecular positioning device carries out binarization processing on each similarity value in the similarity value matrix according to the comparison result so as to obtain a binarization matrix of the target picture.
In this embodiment, the single molecule positioning device is preset with a predetermined matrix, the predetermined matrix and the luminance value matrix have the same number of rows and the same number of columns, and the elements of the predetermined matrix are luminance values. After the single molecule positioning device determines the brightness value matrix corresponding to each pixel point, the similarity value between the brightness value matrix and a preset matrix is calculated for each brightness value matrix, and all the obtained similarity values are used as matrix elements to form a similarity value matrix. The specific implementation of finding the similarity between the two matrices is well known in the art, and will not be described herein.
For example, when the target picture has 512 pixels, as shown in fig. 7, fig. 7 is a schematic diagram of pixel distribution of the target picture, where n is 512, a11Is a pixel point of the first row and the first column, a12Is a pixel point of the first row and the second column, a1nIs the pixel point of the n-th column of the first row, …, annIs the n-th row and the n-th columnThe pixel point of (2). If with a11Corresponding similarity value is S11And a is12Corresponding similarity value is S12，a1nCorresponding similarity value is S1n,., and annCorresponding similarity value is SnnMatrix of similarity values
In this embodiment, the single molecule positioning apparatus is preset with a preset threshold, for example, the preset threshold may be a value greater than 0 and smaller than 1, and the embodiment of the present invention is not limited thereto. And the single-molecule positioning device compares each similarity value in the similarity value matrix with a preset threshold value to obtain a comparison result corresponding to each similarity value. The comparison result may be that the similarity value is greater than a preset threshold, the similarity value is equal to the preset threshold, or the similarity value is less than the preset threshold. And the unimolecular positioning device carries out binarization processing on each similarity value in the similarity value matrix according to the comparison result to obtain a binarization matrix of the target picture.
As an optional implementation manner, the performing, by the single-molecule positioning apparatus, binarization processing on each similarity value in the similarity value matrix according to the comparison result to obtain a binarization matrix of the target picture includes:
and for each similarity value in the similarity value matrix, when the comparison result corresponding to the similarity value is that the similarity value is greater than or equal to a preset threshold value, binarizing the similarity value into 1, and when the comparison result corresponding to the similarity value is that the similarity value is less than the preset threshold value, binarizing the similarity value into 0 to obtain a binarization matrix of the target picture.
In this embodiment, for example, if a 3 × 3 similarity value matrix is used, if S11-S13, S21-S23 are similarity values greater than or equal to a preset threshold value, and S31-S33 are similarity values smaller than the preset threshold value, the obtained binary matrix
S103, determining a first connected component with a vertex value of 1 from the binarization matrix.
In the embodiment of the invention, the single molecule positioning device determines the first connected component with the vertex value of 1 from the binary matrix. For example, if the binary matrix is
The first communication component with a vertex value of 1 comprises 6 vertices, respectively elements of the first and second rows of the matrix X.
And S104, solving the central coordinate of the first connected component through a preset algorithm to serve as a two-dimensional position coordinate of a single molecule.
In the embodiment of the invention, the preset algorithm can be any one of a centroid method and a Gaussian fitting method. The single molecule positioning device obtains the center coordinate of the first connected component through a preset algorithm to serve as the two-dimensional position coordinate of the single molecule. The specific implementation of the single-molecule positioning device for finding the center coordinate of the connected component by the centroid method or the gaussian fitting method is well known in the art, and will not be described herein.
In the method described in fig. 1, the single molecule positioning device determines, for each pixel point of the target picture, a luminance value matrix corresponding to the pixel point, where the luminance value matrix is a matrix of pixel point luminance values having a preset number of rows and a preset number of columns with the luminance value of the pixel point as a center; the single molecule positioning device acquires a binarization matrix of the target picture according to the brightness value matrix, and determines a first connected component with a vertex value of 1 from the binarization matrix; the single molecule positioning device obtains the center coordinate of the first connected component as the two-dimensional position coordinate of the single molecule through a preset algorithm. Therefore, the embodiment of the invention can position single molecules.
Referring to fig. 2, fig. 2 is a schematic flow chart of another single-molecule positioning method disclosed in the embodiment of the present invention. As shown in fig. 2, the single molecule localization method may include the following steps.
S201, the single-molecule positioning device receives a threshold setting instruction input by a user, and the threshold setting instruction carries a threshold.
In the embodiment of the invention, a user can set the preset threshold value on the single-molecule positioning device. The user can input or select the threshold value on the preset threshold value setting interface of the single molecule positioning device. And inputting or selecting the threshold value larger than 0 and smaller than 1 on the preset threshold value setting interface by the user.
S202, the single-molecule positioning device responds to the threshold setting instruction, and the threshold carried by the threshold setting instruction is set as a preset threshold.
By executing the steps S201 and S202, the user can flexibly set the preset threshold value for comparison with the similarity value according to the change of the experiment conditions and the experiment purpose, thereby improving the flexibility of positioning the single molecule.
S203, aiming at each pixel point of the target picture, the single molecule positioning device determines a brightness value matrix corresponding to the pixel point, wherein the brightness value matrix is a matrix which takes the brightness value of the pixel point as the center and has pixel point brightness values with preset row number and preset column number.
S204, the single molecule positioning device calculates the similarity value of each brightness value matrix and a preset matrix to obtain a similarity value matrix.
S205, the single molecule positioning device compares each similarity value in the similarity value matrix with a preset threshold value to obtain a comparison result corresponding to each similarity value.
S206, the single molecule positioning device conducts binarization processing on each similarity value in the similarity value matrix according to the comparison result to obtain a binarization matrix of the target picture.
And S207, determining a first connected component with a vertex value of 1 from the binarization matrix by the single molecule positioning device.
S208, the single molecule positioning device determines the connected components with the vertex number larger than the preset number from the first connected components as target connected components.
In the embodiment of the invention, after the single molecule positioning device determines the first connected components, the connected components with the vertex number larger than the preset number determined from the first connected components are used as target connected components.
S209, the single molecule positioning device calculates the center coordinate of the target connected component as the two-dimensional position coordinate of the single molecule through a preset algorithm.
In the embodiment of the invention, the target connected component is obtained by screening the first connected component, fluorescent molecules with smaller light spots can be filtered, and the efficiency of positioning the coordinate position of the single molecule can be improved by only calculating the central coordinate of the target connected component meeting the requirement.
Referring to fig. 3, fig. 3 is a schematic flow chart of another single-molecule positioning method disclosed in the embodiment of the present invention. As shown in fig. 3, the single molecule localization method may include the following steps.
S301, outputting a positioning algorithm selection interface by the single-molecule positioning device.
In the embodiment of the invention, a user can select an algorithm on the positioning algorithm selection interface to obtain the center coordinate of the first connected component. The user may select the centroid method or the gaussian fit method at the positioning algorithm selection interface.
S302, the single-molecule positioning device receives a positioning algorithm selection instruction input by a user through the positioning algorithm selection interface.
S303, the single-molecule positioning device responds to the positioning algorithm selection instruction, and a centroid method or a Gaussian fitting method selected by the positioning algorithm selection instruction is set as a preset algorithm.
By implementing steps S301 to S303 of the embodiment of the present invention, the user can select an algorithm for obtaining the center coordinates of the first connected component according to the actual situation. When the user wants to obtain the center coordinate more accurately, the center coordinate of the first connected component can be obtained by using a Gaussian fitting method, and when the user wants to obtain the center coordinate quickly, the center coordinate of the first connected component can be obtained by using a centroid method. Through the implementation of the steps S301 to S303 of the embodiment of the invention, the flexibility of single molecule positioning is improved, and the user experience is improved.
S304, aiming at each pixel point of the target picture, the single molecule positioning device determines a brightness value matrix corresponding to the pixel point, wherein the brightness value matrix is a matrix which takes the brightness value of the pixel point as the center and has pixel point brightness values with preset row number and preset column number.
S305, the single molecule positioning device obtains a binarization matrix of the target picture according to the brightness value matrix.
S306, the single molecule positioning device determines a first connected component with a vertex value of 1 from the binarization matrix.
And S307, the single molecule positioning device calculates the center coordinate of the first connected component as the two-dimensional position coordinate of the single molecule through a preset algorithm.
Referring to fig. 4, fig. 4 is a schematic structural diagram of a single-molecule positioning device according to an embodiment of the present invention. The single molecule positioning apparatus shown in fig. 4 may include a determination module 401, an acquisition module 402, and a calculation module 403. Wherein:
the determining module 401 is configured to determine, for each pixel point of a target picture, a luminance value matrix corresponding to the pixel point, where the luminance value matrix is a matrix of pixel point luminance values having a preset number of rows and a preset number of columns and centered on the luminance value of the pixel point.
In the embodiment of the invention, a user can select or import a picture as a target picture in the single-molecule positioning device. The determining module 401 of the single molecule positioning apparatus determines a luminance value matrix corresponding to each pixel point of the target picture. The luminance value matrix corresponding to the pixel point is a matrix taking the luminance value of the pixel point as the center, and the luminance value matrix corresponding to the pixel point is a matrix having pixel point luminance values with preset row numbers and preset column numbers. For example, the luminance value matrix corresponding to the pixel point may be a matrix of 3 × 3, 5 × 5, and 7 × 7 centered on the luminance value of the pixel point, which is not limited in the embodiment of the present invention. The single-molecule positioning device may include, but is not limited to, a smart phone, a tablet computer, a notebook computer, a desktop computer, and other user equipment. The operating system of the user equipment may include, but is not limited to, an Android operating system, an IOS operating system, a Symbian operating system, a Black Berry operating system, a Windows operating system, and the like, and the embodiment of the present invention is not limited thereto.
For example, when the target picture has 512 × 512 pixels, the determining module 401 determines the luminance value matrix corresponding to each pixel of the target picture, and the determining module 401 determines 512 × 512 luminance value matrices in total. As shown in fig. 7, fig. 7 is a schematic diagram of pixel point distribution of a target picture, where n is 512, a11Is a pixel point of the first row and the first column, a12Is a pixel point of the first row and the second column, a1nIs the pixel point of the n-th column of the first row, …, annIs the pixel point of the nth row and the nth column. If the luminance value matrix is a matrix of 3 x 3, the determination module 401 determines a11When the corresponding brightness value matrix is selected from the target picture, the value is selected as a11The central 3 x 3 pixel. In pixel point of target picture with a11The central 3 x 3 pixel point only comprises a12、 a21And a22The determining module 401 will obtain a11、a12、a21And a22And a of the pixel points without the target picture11The brightness value of the pixel point of 3 x 3 as the center is set as 0; determine that the module 401 is to operate at a11The brightness value of the central 3 x 3 pixel point constitutes a11A corresponding matrix of luminance values.
For example, if a11Corresponding brightness value of L11，a12Corresponding brightness value of L12，a21Corresponding brightness value of L21，a22Corresponding brightness value of L22Then is equal to a11Corresponding luminance value matrix A11Is composed of
In the same way as a12Corresponding luminance value matrix A12Is composed of
Wherein L is13Is a13Brightness value of L23Is a23The luminance value of (a). In the same way as a22Corresponding luminance value matrix A22Is composed of
Wherein L is31Is a31Brightness value of L32Is a32Brightness value of L33Is a33The luminance value of (a).
An obtaining module 402, configured to obtain a binarization matrix of the target picture according to the luminance value matrix.
In the embodiment of the present invention, after the determining module 401 determines the luminance value matrix corresponding to each pixel point, the obtaining module 402 obtains the binarization matrix of the target picture according to the determined luminance value matrix.
The determining module 401 is further configured to determine a first connected component with a vertex value of 1 from the binarization matrix.
In this embodiment of the present invention, the determining module 401 determines the first connected component with a vertex value of 1 from the binarization matrix. For example, if the binary matrix is
The first communication component with a vertex value of 1 comprises 6 vertices, respectively elements of the first and second rows of the matrix X.
And a calculating module 403, configured to calculate, by using a preset algorithm, a center coordinate of the first connected component as a two-dimensional position coordinate of a single molecule.
In the embodiment of the invention, the preset algorithm can be any one of a centroid method and a Gaussian fitting method. The calculation module 403 calculates the center coordinate of the first connected component as the two-dimensional position coordinate of the single molecule through a preset algorithm. The specific implementation of the calculating module 403 for finding the center coordinate of the connected component by the centroid method or the gaussian fitting method is well known in the art, and will not be described herein.
Referring to fig. 5, fig. 5 is a schematic structural diagram of another single-molecule positioning device according to an embodiment of the present invention. The single-molecule positioning device shown in fig. 5 is optimized from the single-molecule positioning device shown in fig. 4. Compared with the single molecule positioning device shown in fig. 4, the single molecule positioning device shown in fig. 5 may further include a first receiving module 404 and a first setting module 405 in addition to the modules of the single molecule positioning device shown in fig. 4. The acquiring module 402 shown in fig. 5 includes a first calculating unit 4021, a comparing unit 4022, and a binarizing unit 4023, and the calculating module 403 includes a determining unit 4031 and a second calculating unit 4032. Wherein:
the first calculating unit 4021 is configured to calculate a similarity value between each of the luminance value matrices and a preset matrix to obtain a similarity value matrix.
A comparing unit 4022, configured to compare each similarity value in the similarity value matrix with a preset threshold, and obtain a comparison result corresponding to each similarity value.
A binarization unit 4023, configured to perform binarization processing on each similarity value in the similarity value matrix according to the comparison result, to obtain a binarization matrix of the target picture.
In the embodiment of the invention, the monomolecular positioning device is preset with the preset matrix, the preset matrix and the brightness value matrix have the same row number and the same column number, and the elements of the preset matrix are brightness values. After the determining module 401 determines the luminance value matrix corresponding to each pixel point, the first calculating unit 4021 calculates the similarity value between the luminance value matrix and the preset matrix for each luminance value matrix, and uses all the obtained similarity values as matrix elements to form a similarity value matrix. The specific implementation of finding the similarity between the two matrices is well known in the art, and will not be described herein.
For example, when the target picture has 512 pixels, as shown in fig. 7, fig. 7 is a schematic diagram of pixel distribution of the target picture, where n is 512, a11Is a pixel point of the first row and the first column, a12Is a pixel point of the first row and the second column, a1nIs the pixel point of the n-th column of the first row, …, annIs the pixel point of the nth row and the nth column. If with a11Corresponding similarity value is S11And a is12Corresponding similarity value is S12，a1nCorresponding similarity value is S1n,., and annCorresponding similarity value isSnnMatrix of similarity values
In the embodiment of the present invention, the single molecule positioning apparatus is preset with a preset threshold, for example, the preset threshold may be a value greater than 0 and smaller than 1, and the embodiment of the present invention is not limited. The comparing unit 4022 compares each similarity value in the similarity value matrix with a preset threshold to obtain a comparison result corresponding to each similarity value. The comparison result may be that the similarity value is greater than a preset threshold, the similarity value is equal to the preset threshold, or the similarity value is less than the preset threshold. The binarization unit 4023 performs binarization processing on each similarity value in the similarity value matrix according to the comparison result to obtain a binarization matrix of the target picture.
As an optional implementation manner, the binarization unit 4023 is specifically configured to:
and for each similarity value in the similarity value matrix, when the comparison result corresponding to the similarity value is that the similarity value is greater than or equal to the preset threshold value, binarizing the similarity value into 1, and when the comparison result corresponding to the similarity value is that the similarity value is less than the preset threshold value, binarizing the similarity value into 0 to obtain the binarization matrix of the target picture.
In this embodiment, for example, if a 3 × 3 similarity value matrix is used, if S11-S13, S21-S23 are similarity values greater than or equal to a preset threshold value, and S31-S33 are similarity values smaller than the preset threshold value, the obtained binary matrix
A first receiving module 404, configured to receive a threshold setting instruction input by a user before the determining module 401 determines, for each pixel point of the target picture, a luminance value matrix corresponding to the pixel point, where the threshold setting instruction carries a threshold.
In the embodiment of the invention, a user can set the preset threshold value on the single-molecule positioning device. The user can input or select the threshold value on the preset threshold value setting interface of the single molecule positioning device. And inputting or selecting the threshold value larger than 0 and smaller than 1 on the preset threshold value setting interface by the user.
A first setting module 405, configured to respond to the threshold setting instruction, and set a threshold carried by the threshold setting instruction to a preset threshold.
By implementing the embodiment of the invention, a user can flexibly set the preset threshold value for comparing with the similarity value according to the change of the experimental conditions and the experimental purpose, thereby improving the flexibility of positioning single molecules.
A determining unit 4031, configured to determine, as target connected components, connected components with a vertex number greater than a preset number from the first connected components.
In this embodiment of the present invention, after the determining module 401 determines the first connected components, the determining unit 4031 determines the connected components with the vertex number greater than the preset number from the first connected components as the target connected components.
And the second calculation unit 4032 is configured to calculate, through a preset algorithm, a center coordinate of the target connected component as a two-dimensional position coordinate of a single molecule.
In the embodiment of the present invention, the target connected components are obtained by screening the first connected components, fluorescent molecules with small light spots can be filtered, and the second calculation unit 4032 only calculates the center coordinates of the target connected components meeting the requirements, so that the efficiency of positioning the coordinate positions of the single molecules can be improved.
Referring to fig. 6, fig. 6 is a schematic structural diagram of another single-molecule positioning device according to an embodiment of the present invention. The single-molecule positioning device shown in fig. 6 is optimized from the single-molecule positioning device shown in fig. 4. Compared with the single molecule positioning device shown in fig. 4, the single molecule positioning device shown in fig. 6 may further include an output module 406, a second receiving module 407 and a second setting module 408 in addition to the modules of the single molecule positioning device shown in fig. 4. Wherein:
an output module 406, configured to output a positioning algorithm selection interface before the calculation module 403 finds, through a preset algorithm, a center coordinate of the first connected component as a two-dimensional position coordinate of a single molecule.
In the embodiment of the invention, a user can select an algorithm on the positioning algorithm selection interface to obtain the center coordinate of the first connected component. The user may select the centroid method or the gaussian fit method at the positioning algorithm selection interface.
And the second receiving module 407 is configured to receive a positioning algorithm selection instruction input by the user through the positioning algorithm selection interface.
And a second setting module 408, configured to, in response to the positioning algorithm selection instruction, set the centroid method or the gaussian fitting method selected by the positioning algorithm selection instruction as a preset algorithm.
By implementing the embodiment of the invention, the user can select the algorithm for calculating the center coordinate of the first connected component according to the actual situation. When the user wants to obtain the center coordinate more accurately, the center coordinate of the first connected component can be obtained by using a Gaussian fitting method, and when the user wants to obtain the center coordinate quickly, the center coordinate of the first connected component can be obtained by using a centroid method. By implementing the embodiment of the invention, the flexibility of single molecule positioning is improved, and the user experience is improved.
In the single-molecule positioning device described in fig. 4 to 6, the determining module determines, for each pixel point of the target picture, a luminance value matrix corresponding to the pixel point, where the luminance value matrix is a matrix of pixel point luminance values having a preset number of rows and a preset number of columns with the luminance value of the pixel point as a center; the obtaining module obtains a binarization matrix of the target picture according to the brightness value matrix; the determining module determines a first connected component with a vertex value of 1 from the binarization matrix; and the calculation module calculates the center coordinate of the first connected component as the two-dimensional position coordinate of the single molecule through a preset algorithm. Therefore, the embodiment of the invention can position single molecules.
It should be noted that, in the foregoing embodiments, the descriptions of the respective embodiments have respective emphasis, and reference may be made to relevant descriptions of other embodiments for parts that are not described in detail in a certain embodiment. Further, those skilled in the art should also appreciate that the embodiments described in the specification are preferred embodiments and that the acts and modules referred to are not necessarily required by the invention.
The steps in the method of the embodiment of the invention can be sequentially adjusted, combined and deleted according to actual needs.
The modules or units in the single molecule positioning device can be combined, divided and deleted according to actual needs.
Those skilled in the art will appreciate that all or part of the steps in the methods of the above embodiments may be implemented by a program instructing hardware associated with the terminal device, where the program may be stored in a computer-readable storage medium, and the storage medium may include: flash disks, Read-Only memories (ROMs), Random Access Memories (RAMs), magnetic or optical disks, and the like.
The above detailed description is provided for a single-molecule positioning method and a single-molecule positioning device disclosed in the embodiments of the present invention, and the specific examples are applied herein to explain the principle and the implementation of the present invention, and the description of the above embodiments is only used to help understanding the method and the core concept of the present invention; meanwhile, for a person skilled in the art, according to the idea of the present invention, there may be variations in the specific embodiments and the application scope, and in summary, the content of the present specification should not be construed as a limitation to the present invention.
Claims (6)
1. A single molecule positioning apparatus, comprising:
the determining module is used for determining a brightness value matrix corresponding to each pixel point of a target picture, wherein the brightness value matrix is a matrix which takes the brightness value of the pixel point as a center and has pixel point brightness values with preset line number and preset column number;
the obtaining module is used for obtaining a binarization matrix of the target picture according to the brightness value matrix;
the determining module is further configured to determine a first connected component with a vertex value of 1 from the binarization matrix;
and the calculation module is used for solving the central coordinate of the first connected component through a preset algorithm to serve as the two-dimensional position coordinate of the single molecule.
2. The single molecule positioning apparatus of claim 1, wherein the obtaining module comprises:
the first calculation unit is used for calculating the similarity value of each brightness value matrix and a preset matrix to obtain a similarity value matrix;
the comparison unit is used for comparing each similarity value in the similarity value matrix with a preset threshold value to obtain a comparison result corresponding to each similarity value;
and the binarization unit is used for carrying out binarization processing on each similarity value in the similarity value matrix according to the comparison result so as to obtain a binarization matrix of the target picture.
3. The single-molecule positioning device according to claim 2, wherein the binarization unit is specifically configured to:
and for each similarity value in the similarity value matrix, when the comparison result corresponding to the similarity value is that the similarity value is greater than or equal to the preset threshold value, binarizing the similarity value into 1, and when the comparison result corresponding to the similarity value is that the similarity value is less than the preset threshold value, binarizing the similarity value into 0 to obtain the binarization matrix of the target picture.
4. The single molecule positioning apparatus of claim 2 or 3, further comprising:
the first receiving module is used for receiving a threshold setting instruction input by a user before the determining module determines a brightness value matrix corresponding to each pixel point of the target picture, wherein the threshold setting instruction carries a threshold;
and the first setting module is used for responding to the threshold setting instruction and setting the threshold carried by the threshold setting instruction as a preset threshold.
5. The single-molecule positioning apparatus according to any one of claims 1 to 3, wherein the calculation module comprises:
a determining unit, configured to determine, as a target connected component, connected components having a number of vertices greater than a preset number from the first connected components;
and the second calculation unit is used for solving the central coordinate of the target connected component through a preset algorithm to serve as the two-dimensional position coordinate of the single molecule.
6. The single-molecule positioning device according to any one of claims 1 to 3, wherein the predetermined algorithm comprises any one of a centroid method and a Gaussian fitting method, and the single-molecule positioning device further comprises:
the output module is used for outputting a positioning algorithm selection interface before the calculation module obtains the center coordinate of the first connected component as the two-dimensional position coordinate of the single molecule through a preset algorithm;
the second receiving module is used for receiving a positioning algorithm selection instruction input by a user through the positioning algorithm selection interface;
and the second setting module is used for responding to the positioning algorithm selection instruction and setting the centroid method or the Gaussian fitting method selected by the positioning algorithm selection instruction as a preset algorithm.
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| CN201911012189.5A CN110889825A (en) | 2015-08-07 | 2015-08-07 | Single molecule positioning device |
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| CN101751572A (en) * | 2008-12-05 | 2010-06-23 | 比亚迪股份有限公司 | Pattern detection method, device, equipment and system |
| CN104156951A (en) * | 2014-07-30 | 2014-11-19 | 电子科技大学 | Leukocyte detecting method aiming at bronchoalveolar lavage smear |
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| CN101739548B (en) * | 2009-02-11 | 2012-07-25 | 北京智安邦科技有限公司 | Eye detection method and system |
| CN102129553A (en) * | 2011-03-16 | 2011-07-20 | 上海交通大学 | Method for eye detection based on single infrared light supply |
| CN102663354B (en) * | 2012-03-26 | 2014-02-19 | 腾讯科技（深圳）有限公司 | Face calibration method and system thereof |
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| CN101751572A (en) * | 2008-12-05 | 2010-06-23 | 比亚迪股份有限公司 | Pattern detection method, device, equipment and system |
| CN104156951A (en) * | 2014-07-30 | 2014-11-19 | 电子科技大学 | Leukocyte detecting method aiming at bronchoalveolar lavage smear |
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