WO2017025001A1

WO2017025001A1 - Single molecule localisation apparatus, method, and system

Info

Publication number: WO2017025001A1
Application number: PCT/CN2016/093737
Authority: WO
Inventors: 葛良进; 曾健明; 曾立董
Original assignee: 深圳市瀚海基因生物科技有限公司
Priority date: 2015-08-07
Filing date: 2016-08-05
Publication date: 2017-02-16

Abstract

A single molecule localisation method, apparatus, and system, the single molecule localisation method comprising: acquiring a luminance value matrix of each pixel point of a target image, the luminance value matrix being a pixel point luminance value matrix centred on pixel point luminance value and having a preset number of lines and a preset number of columns (S101); comparing the luminance value matrix with a preset matrix, and eliminating the pixel points corresponding to a luminance value matrix having a degree of similarity less than a first threshold (S102); and implementing localisation of the remaining pixel points to implement single molecule localisation (S103). Thus, the present method is able to implement localisation of a single molecule.

Description

Single molecule positioning device, method and system

The present application claims the priority and benefit of the priority of the priority of the disclosure of the priority of the disclosure of the disclosure of the disclosure of the disclosure of the disclosure of the entire disclosure of

Technical field

The present invention relates to the field of computer technologies, and in particular, to a single molecule positioning device, method and system.

Background technique

In recent years, super-resolution fluorescence imaging technology has realized the observation of the fine structure of living cells at the molecular level, and has become an extremely important tool for biological structure and functional imaging, and has become an indispensable part of single-molecule sequencing technology. Super-resolution fluorescence imaging technology is a technique for visually displaying the spatial distribution of single molecules (ie, single molecules) at a spatial resolution of nanometer scale. Super-resolution fluorescence imaging can be used to study the interaction between single molecules labeled by fluorescent molecules, and can be used to determine the extension of bases in single-molecule sequencing technology.

The commonly used super-resolution fluorescence imaging method is a microscopic imaging technique that utilizes the switching effect of a fluorescent molecule itself to perform positioning. For example, photosensitive localization microscopy (PALM), random optical reconstruction microscopy (STORM), etc., which acquire localized information of sparsely distributed single molecules labeled with fluorescent molecules at different times, and then superimpose the positioning information obtained at different times. Ultimately achieve high lateral nano resolution. A super-resolution image is obtained by superimposing several single-molecular positions. Obviously, single molecule localization is an indispensable part of the super-resolution fluorescence imaging process. Therefore, it is very important to provide a device capable of positioning a single molecule.

Summary of the invention

Embodiments of the present invention disclose a single molecule positioning device, method and system capable of positioning a single molecule.

In a first aspect, an embodiment of the present invention discloses a single molecule positioning method, and the single molecule positioning Methods include:

Obtaining a matrix of luminance values of each pixel of the target image, wherein the matrix of luminance values is a matrix having a preset number of rows and a pixel value of the preset number of columns, centered on the luminance value of the pixel;

Comparing the brightness value matrix with the preset matrix, and removing pixel points corresponding to the brightness value matrix whose similarity is less than the first threshold;

The remaining pixels are positioned to achieve the single molecule positioning.

In a possible implementation, the comparing the luminance value matrix and the preset matrix, and removing the pixel points corresponding to the luminance value matrix whose similarity is less than the first threshold, includes:

Calculating a similarity value of each of the brightness value matrix and the preset matrix to obtain a similarity value matrix;

Comparing each element of the similarity value matrix with a size of the first threshold, and removing a pixel point corresponding to an element of the similarity value matrix that is smaller than the first threshold.

In a possible implementation manner, the method further includes: removing a pixel point corresponding to an element of the similarity value matrix that is greater than a third threshold, where the third threshold is greater than the first threshold.

In a possible implementation, the size of each element in the comparison similarity value matrix and the first threshold is removed, and the pixel corresponding to the element smaller than the first threshold in the similarity value matrix is removed, including :

Comparing the size of each element in the similarity value matrix with a first threshold;

Assigning an element of the similarity value matrix that is greater than or equal to the first threshold to a, and assigning an element of the similarity value matrix that is smaller than the first threshold to b, to obtain a binary value a matrix, the elements in the binarization matrix being selected from one of the a and the b, the a is not equal to the b;

The pixel points corresponding to the element b in the binarization matrix are removed.

In a possible implementation manner, before or after removing the pixel point corresponding to the element b in the binarization matrix, the method includes:

Determining a connected component of the element a in the binarization matrix;

The pixel points corresponding to all the elements in the connected component whose element a is smaller than the second threshold are removed.

In a possible implementation manner, after the determining the connected component of the element a in the binarization matrix, the method further includes:

The pixel point corresponding to all the elements in the connected component whose element a is greater than the fourth threshold is removed, and the fourth threshold is greater than the second threshold.

In a possible implementation manner, the positioning the remaining pixels includes:

Determining, by a preset algorithm, a center coordinate of a connected component of the element a in the binarization matrix corresponding to the remaining pixel points to determine coordinates of the single molecule.

In a possible implementation manner, the preset algorithm is selected from at least one of a centroid method, a Gaussian fitting method, a maximum likelihood method, a solution linear equation method, and a Ma Liang algorithm.

In a possible implementation manner, the preset algorithm is at least one of a centroid method and a Gaussian fitting method.

In a possible implementation, before the determining, by the preset algorithm, the center coordinates of the connected component of the element a in the binarization matrix corresponding to the remaining pixel points, the method further includes:

Output positioning algorithm selection interface;

Receiving a positioning algorithm selection instruction input by the user through the positioning algorithm selection interface;

And in response to the positioning algorithm selection instruction, setting an algorithm selected by the positioning algorithm selection instruction as a preset algorithm.

In a possible implementation, before the obtaining a matrix of luminance values of each pixel of the target image, the method further includes:

Receiving a threshold input instruction input by a user, the threshold setting instruction carrying a threshold;

The threshold carried by the threshold setting instruction is set to a first threshold, a second threshold, a third threshold, and/or a fourth threshold in response to the threshold setting instruction.

In a second aspect, embodiments of the present invention disclose a single molecule positioning device having the functionality to implement the first aspect or the possible implementation of the first aspect. This function can be implemented in hardware or in hardware by executing the corresponding software. The hardware or software includes one or more units corresponding to the functions described above. The unit can be software and/or hardware.

In a third aspect, an embodiment of the present invention discloses a single molecule positioning apparatus, including a processor and a memory, wherein the memory is connected to the processor, wherein the memory stores a set of program codes, and the processor is used to call the memory. The stored program code performs the method provided by the first aspect described above or a possible implementation of the first aspect.

In a fourth aspect, an embodiment of the present invention discloses a system including a processor and a memory, where The memory is coupled to the processor, wherein the memory stores a set of program code for calling program code stored in the memory to perform the method provided by the first aspect or the possible implementation of the first aspect the way.

In a fifth aspect, an embodiment of the present invention discloses a computer readable storage medium storing one or more programs, where one or more programs include instructions that, when executed by a single molecule positioning device, cause a single molecule positioning device to perform the above A method provided on the one hand or a possible implementation of the first aspect.

In the embodiment of the present invention, after obtaining the luminance value matrix of each pixel of the target image, the single molecule positioning device compares the luminance value matrix with the preset matrix, and removes the pixel corresponding to the luminance value matrix whose similarity is smaller than the first threshold. Then, the remaining pixels are positioned to achieve single molecule positioning. It can be seen that embodiments of the invention are capable of locating a single molecule.

DRAWINGS

In order to more clearly illustrate the technical solutions in the embodiments of the present invention, the drawings used in the embodiments will be briefly described below. It is obvious that the drawings in the following description are some embodiments of the present invention. Those skilled in the art can also obtain other drawings based on these drawings without paying any creative work.

1 is a schematic flow chart of a single molecule positioning method disclosed in an embodiment of the present invention;

2 is a schematic diagram of pixel point distribution of a target picture disclosed in an embodiment of the present invention;

3 is a schematic flow chart of another single molecule positioning method disclosed in an embodiment of the present invention;

4 is a schematic structural view of a single molecule positioning device according to an embodiment of the present invention;

FIG. 5 is a schematic structural diagram of another single molecule positioning device according to an embodiment of the present invention; FIG.

FIG. 6 is a schematic structural diagram of another single molecule positioning device disclosed in an embodiment of the present invention.

detailed description

The technical solutions in the embodiments of the present invention are clearly and completely described in the following with reference to the accompanying drawings in the embodiments of the present invention. It is obvious that the described embodiments are a part of the embodiments of the present invention, but not all embodiments. All other embodiments obtained by those skilled in the art based on the embodiments of the present invention without creative efforts are within the scope of the present invention.

Embodiments of the present invention disclose a single molecule positioning method, a single molecule positioning device, and a system, which are capable of Positioning a single molecule. The details are described below separately.

The single molecule positioning device according to the embodiment of the present invention may be displayed in the form of software and/or hardware. The software form includes but is not limited to various machine executable code or programs, and may be stored in a machine readable medium, the machine readable medium. This includes but is not limited to read only memory, random access memory, magnetic disks, and optical disks. Hardware forms include, but are not limited to, smartphones, tablets, laptops, desktops, and the like. The operating system of the single-molecular positioning device may include, but is not limited to, an Android operating system, an IOS operating system, a Symbian operating system, a Blackberry operating system, a Windows operating system, etc., which are not limited by the embodiment of the present invention. .

Please refer 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 positioning method may include the following steps.

S101. The single molecule positioning device obtains a matrix of luminance values of each pixel of the target image.

In the embodiment of the present invention, the user can select or import a picture as a target picture in the single molecule positioning device.

Optionally, the pixel may be a small square after dividing the target image into a plurality of small squares, and a small square is one of the above pixels. Alternatively, the above pixel points may also be bright spots in the target picture.

Optionally, the matrix of luminance values of one pixel may be a matrix having a preset number of rows and a pixel value of the preset number of columns centered on the luminance value of the pixel. Optionally, the brightness value matrix may also refer to a signal intensity distribution matrix, a fluorescence intensity distribution matrix, or a fluorescence intensity matrix collected by a camera in each FOV (filed of view).

For example, the matrix of the luminance value of the pixel may be a matrix of 3*3, 5*5, and 7*7 centered on the luminance value of the pixel, which is not limited in the embodiment of the present invention.

For example, when the target picture has 512*512 pixels, the single molecule positioning device determines the matrix of luminance values for each pixel of the target picture, and the single molecule positioning device will determine a total of 512*512 brightness value matrices. As shown in FIG. 2, FIG. 2 is a schematic diagram of pixel point distribution of a target picture, where n is 512, a ₁₁ is a pixel of the first row and the first column, and a ₁₂ is a pixel of the first row and the second column, a _1n For the pixel of the nth column of the first row, ..., a _nn is the pixel of the nth row and the nth column. , Then a monomolecular positioning means determines the luminance value corresponding to a ₁₁ matrix when the matrix is the luminance value of 3 * 3 matrix, the pixels from the target image selected as the center point of a ₁₁ to 3 * 3. The 3*3 pixel centered at a ₁₁ in the pixel of the target picture includes only a ₁₂ , a ₂₁ and a ₂₂ , and the single molecule positioning device will acquire the brightness of a ₁₁ , a ₁₂ , a ₂₁ and a ₂₂ Value, and set the luminance value of the 3*3 pixel point centered on a ₁₁ in the pixel where there is no target picture to 0; the single molecule positioning device will 3*3 pixel point centered on a ₁₁ a ₁₁ constituting a luminance value corresponding to the luminance values of the matrix.

For example, if the brightness value corresponding to a ₁₁ is L ₁₁ , the brightness value corresponding to a ₁₂ is L ₁₂ , the brightness value corresponding to a ₂₁ is L ₂₁ , and the brightness value corresponding to a ₂₂ is L ₂₂ , then the brightness corresponding to a ₁₁ Value matrix A ₁₁ is

Similarly, with a ₁₂ corresponding to the luminance value of the matrix A ₁₂

Where L ₁₃ is the luminance value of a ₁₃ and L ₂₃ is the luminance value of a ₂₃ . Similarly, a ₂₂ and a luminance value corresponding to the matrix A ₂₂

Where L ₃₁ is the luminance value of a ₃₁ , L ₃₂ is the luminance value of a ₃₂ , and L ₃₃ is the luminance value of a ₃₃ .

S102. The single molecule positioning device compares the brightness value matrix with the preset matrix, and removes pixel points corresponding to the brightness value matrix whose similarity is less than the first threshold.

For example, as shown in FIG. 2, if the similarity between the luminance value matrix of the pixel point a ₁₁ and the preset matrix is less than the first threshold, the pixel point a _{11 is} removed; if the luminance value matrix of the pixel point a ₁₂ and the preset matrix If the similarity is less than the first threshold, the pixel point a ₁₂ is also removed.

S103. The single molecule positioning device positions the remaining pixels to achieve single molecule positioning.

In the embodiment of the present invention, the remaining pixel points are pixels corresponding to the brightness value matrix whose similarity is greater than or equal to the first threshold, and the remaining pixel points may be regarded as the pixel points corresponding to the image of the single molecule in the target picture. By removing the pixel points corresponding to the luminance value matrix whose similarity is smaller than the first threshold, the interference image in the target image can be removed, and the position of the single molecule image in the target image can be accurately determined.

It can be seen that by implementing the method described in FIG. 1, the single molecule positioning device can filter the non-single molecule image in the target picture, thereby obtaining the position of the single molecule image in the target picture.

As an optional implementation manner, step S102 may specifically include the following steps:

11) The single molecule positioning device calculates a similarity value between each brightness value matrix and the preset matrix to obtain a similarity value matrix;

12) The single molecule positioning device compares each element in the similarity value matrix with the size of the first threshold, and removes pixels corresponding to the elements of the similarity value matrix that are smaller than the first threshold.

For example, as shown in FIG. 2, FIG. 2 is a schematic diagram of pixel point distribution of a target picture, where n is 512, if the luminance value matrix of a ₁₁ and the preset matrix have similarity values of S ₁₁ , a ₁₂ brightness value The similarity value between the matrix and the preset matrix is S ₁₂ , the similarity value of the brightness value matrix of the a _1n and the preset matrix is S _1n ,..., the similarity value of the brightness value matrix of the a _nn and the preset matrix is S _nn , the similarity value matrix

The single molecule positioning device compares S ₁₁ , S ₁₂ , . . . , S _nn with the first threshold, and removes the pixel points corresponding to the elements of the S ₁₁ , S ₁₂ , . . . , S _nn that are smaller than the first threshold. In this embodiment, one element in the similarity value matrix corresponds to a matrix of luminance values. A matrix of luminance values corresponds to one pixel. Therefore, the elements in the similarity value matrix correspond one-to-one with the pixel points. If _{_{S 11, S 12, ...,}} S nn in S ₁₁ and S ₁₂ is smaller than a first threshold, a ₁₁ and a ₁₂ removed.

As an optional implementation manner, after the single molecule positioning device compares each element in the similarity value matrix with the first threshold value in step 12), the third similarity value matrix may be removed from the similarity value matrix. The pixel corresponding to the element, the third threshold being greater than the first threshold. The principle that the single-molecular locating device removes the pixel points corresponding to the elements of the similarity value matrix that are greater than the third threshold is similar to the principle of removing the pixel points corresponding to the elements of the similarity value matrix that are smaller than the first threshold, and details are not described herein. The first threshold and/or the third threshold are set based on the degree of similarity between the fluorescence signal intensity distribution matrix on the actually obtained image and the fluorescence signal intensity distribution matrix mathematically fitted under the same machine parameter conditions.

As an optional implementation manner, as shown in FIG. 3, the foregoing step 12) may specifically include steps S303-S305, that is,

S303. The single molecule positioning device compares each element in the similarity value matrix with a size of the first threshold.

S304. The single molecule positioning device assigns an element of the similarity value matrix that is greater than or equal to the first threshold to a, and assigns an element of the similarity value matrix that is smaller than the first threshold to b, to obtain a binarization matrix. .

S305. The single molecule positioning device removes pixel points corresponding to the element b in the binarization matrix.

In this embodiment, wherein the elements in the binarization matrix are selected from one of a and b. Optional , a can be 1, b can be 0, or a and b can be other values, a is not equal to b.

In this embodiment, the first threshold may be a value greater than 0 and less than 1, which is not limited in the embodiment of the present invention.

In this embodiment, a similarity value matrix of 3*3 is used as an example. If S11-S13, S21-S23 are similarity values greater than or equal to a preset threshold, S31-S33 are similar to a preset threshold. Degree value, a is 1 and b is 0, then the obtained binarization matrix

In this embodiment, the elements in the binarization matrix correspond one-to-one with the elements in the similarity value matrix, and one luminance value matrix corresponds to one element in the similarity value matrix. A matrix of luminance values corresponds to one pixel. Therefore, the elements in the binarization matrix correspond one-to-one with the pixel points.

In this embodiment, the single molecule positioning device removes the pixel points corresponding to the element having a value of 0 in the binarization matrix X.

As an optional implementation manner, as shown in FIG. 3, after removing the pixel points corresponding to the element b in the binarization matrix, the single molecule positioning device may further perform steps S306 and S307, namely:

S306. The single molecule positioning device determines a connected component of the element a in the binarization matrix.

S307. The single molecule positioning device removes a pixel point corresponding to all elements in the connected component whose number of elements a is smaller than the second threshold.

The so-called connected component can be regarded as a matrix, also called a connected region or a connected domain, which can be defined as: centered on an element (value) a in the matrix, and the surrounding eight values (elements) are connected. Such as matrix X1

bb	aa	bb
aa	aa	bb
bb	bb	aa

,

Bold and italic is the central element a, and the surrounding 8 elements can be called the neighborhood of the central element a; if there are other elements a in the eight neighborhoods of the center a of the matrix X1, then the two a (corresponding pixels) Point) A connected domain, and so on. If there are other pixels with a value of a in the eight neighborhoods of the two pixels, the connected domain is gradually expanded until there is no unstated value in the eight neighborhoods of all the pixels. Pixels. The following example is a region with a value of 1 (ie a=1, bold and italic), which is a connected domain, the inner frame shows a connected domain, and b takes 0:

In this embodiment, for example, if the connected component of a in the binarization matrix M includes the connected component 1 and the connected component 2, the connected component 1 includes 2 elements corresponding to the pixel point a ₁₁ and a ₁₂ . The connected component 2 includes four elements corresponding to the pixel points a ₂₁ to a _{24 , respectively} . The second threshold is 3, and the single molecule positioning device removes a ₁₁ and a ₁₂ .

As an optional implementation manner, after the single-molecular positioning device performs step S306, the pixel corresponding to all the elements in the connected component whose number of elements a is greater than the fourth threshold may be removed, and the fourth threshold is greater than the second Threshold. The principle that the single molecule positioning device removes the pixel points corresponding to all the elements in the connected component whose number of elements a is greater than the fourth threshold is similar to the principle of removing the pixel points corresponding to all the elements in the connected component whose number of elements a is smaller than the second threshold. This will not go into details. The setting of the second threshold and/or the fourth threshold is based on the size of the single-molecule spot, and the two thresholds are simultaneously set, that is, determining the upper and lower limits to determine a range of values, which enables the setting of the sequencer system, particularly the optical/electrical system parameter setting. In the case of a single molecule, the single molecule fluorescence peaks are determined more accurately.

As an optional implementation manner, the specific implementation manner of the foregoing S103 may be the step S308 shown in FIG. 3, that is,

S308. The single molecule positioning device determines a center coordinate of a connected component of the element a in the binarization matrix corresponding to the remaining pixel points by using a preset algorithm to determine a coordinate of the single molecule.

In this embodiment, for example, if the connected component of a in the binarization matrix M includes the connected component 1, the connected component 2, and the connected component 3, the connected component 1 includes 2 elements, and the connected component 2 Including 4 elements, the connected component 3 includes 6 elements, the second threshold is 3, and the fourth threshold is 5, the single molecule positioning device removes the pixel points corresponding to all the elements of the connected component 1 and the connected component 3, and then passes the pre- Let the algorithm determine the center coordinates of the connected component 2 to determine the coordinates of the single molecule.

As an optional implementation manner, the preset algorithm is selected from at least one of a centroid method, a Gaussian fitting method, a maximum likelihood method, a solution linear equation method, and a Ma Liang algorithm.

By performing steps S306-S308 of the embodiment of the present invention, the connected components are filtered, and the fluorescent molecules with small spots can be filtered out, and only the central coordinates of the connected components that meet the requirements are calculated, thereby improving the efficiency of positioning the coordinate positions of the single molecules. .

As an optional implementation manner, as shown in FIG. 3, before the single molecule positioning device determines the center coordinate of the connected component of the element a in the binarization matrix corresponding to the remaining pixel points by the preset algorithm, the single molecule positioning device Steps S309 to S311 can also be performed, namely:

S309. The single molecule positioning device outputs a positioning algorithm selection interface.

S310. The single molecule positioning device receives a positioning algorithm selection instruction input by a user through a positioning algorithm selection interface.

S311: The single molecule positioning device responds to the positioning algorithm selection instruction, and sets an algorithm for selecting the positioning algorithm selection instruction as a preset algorithm.

In this embodiment, the positioning algorithm selection interface may include a selection of at least two algorithms of a centroid method, a Gaussian fitting method, a maximum likelihood method, a solution linear equation method, and a Ma Liang algorithm, and the user may select an interface in the positioning algorithm. An algorithm is selected as the preset algorithm to find the center coordinates of the connected components.

By performing steps S309-S311 of the embodiment of the present invention, the user can select an algorithm for determining the center coordinates of the connected components according to actual conditions. When the user wants a more accurate center coordinate, the Gaussian fitting method can be used to find the center coordinate of the connected component; when the user wants to quickly obtain the center coordinate, the centroid method can be used to find the center coordinate of the connected component. Therefore, by implementing steps S309-S311 of the embodiment of the present invention, the flexibility of single-molecule positioning is improved, and the user experience is improved.

As an optional implementation manner, as shown in FIG. 3, before obtaining the matrix of luminance values of each pixel of the target image, the single molecule positioning device may further perform steps S312 and S313, namely:

S312. The single molecule positioning device receives a threshold setting instruction input by a user, and the threshold setting instruction carries a threshold.

S313. The single molecule positioning device responds to the threshold setting instruction, and sets the threshold value carried by the threshold setting instruction. The first threshold and/or the second threshold are set.

Optionally, if the single-molecular positioning device further removes the pixel corresponding to the element of the similarity value matrix that is greater than the third threshold, the single-molecule positioning device may also set the threshold value carried by the threshold setting instruction to the first threshold and the second threshold. And / or a third threshold.

Optionally, if the single molecular positioning device further removes the pixel corresponding to all the elements in the connected component of the fourth threshold, the single molecule positioning device may also set the threshold carried by the threshold setting instruction to the first threshold, The second threshold and/or the fourth threshold.

By performing steps S312 and S313, the user can flexibly set the first threshold value compared with the similarity value according to the change of the experimental conditions and the experimental purpose, thereby improving the flexibility of single molecule positioning.

Please refer 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 device shown in FIG. 4 may include an acquisition module 401, a removal module 402, and a positioning module 403. among them:

The obtaining module 401 is configured to obtain a matrix of luminance values of each pixel of the target image, where the matrix of luminance values is a matrix having a preset row number and a preset column number of pixel point luminance values centered on the luminance value of the pixel point. .

The removing module 402 is configured to compare the luminance value matrix with the preset matrix, and remove pixel points corresponding to the luminance value matrix whose similarity is less than the first threshold.

The positioning module 403 is configured to locate the remaining pixels to achieve single molecule positioning.

Please refer to FIG. 5 together. FIG. 5 is a schematic structural diagram of another single molecule positioning device disclosed in an embodiment of the present invention. The single molecule positioning device shown in FIG. 5 is optimized by 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 determining module 404, an output module 405, and a first in addition to the module of the single molecule positioning device shown in FIG. The receiving module 406, the first setting module 407, the second receiving module 408, and the second setting module 409. The removal module 402 shown in FIG. 5 includes a calculation unit 4021 and a comparison unit 4022. among them:

The calculating unit 4021 is configured to calculate a similarity value between each matrix of luminance values and a preset matrix to obtain a matrix of similarity values.

The comparing unit 4022 is configured to compare the size of each element in the similarity value matrix with the first threshold, and remove the pixel corresponding to the element in the similarity value matrix that is smaller than the first threshold.

As an optional implementation manner, the comparing unit 4022 is further configured to remove a pixel corresponding to the element that is greater than the third threshold in the similarity value matrix, where the third threshold is greater than the first threshold.

As an optional implementation manner, the comparing unit 4022 compares the size of each element in the similarity value matrix with the first threshold, and removes the pixel corresponding to the element smaller than the first threshold in the similarity value matrix, which may be: a size of each element in the similarity value matrix and a first threshold; an element of the element of the similarity value matrix that is greater than or equal to the first threshold is assigned a, and an element of the similarity value matrix is smaller than the first threshold The value is assigned to b to obtain a binarization matrix. The elements in the binarization matrix are selected from one of a and b, and a is not equal to b; the pixel corresponding to the element b in the binarization matrix is removed.

The determining module 404 is configured to determine a connected component of the element a in the binarization matrix before or after the comparing unit 4022 removes the pixel point corresponding to the element b in the binarization matrix.

The removing module 402 is further configured to remove pixel points corresponding to all elements in the connected component whose number of elements a is less than the second threshold.

The removing module 402 is further configured to remove a pixel point corresponding to all elements in the connected component whose number of elements a is greater than a fourth threshold, where the fourth threshold is greater than the second threshold.

The positioning module 403 is specifically configured to: determine, by using a preset algorithm, a center coordinate of a connected component of the element a in the binarization matrix corresponding to the remaining pixel points to determine a coordinate of the single molecule.

As an optional implementation manner, the preset algorithm is at least one of a centroid method and a Gaussian fitting method.

The output module 405 is configured to output a positioning algorithm selection interface before the positioning module 403 determines the center coordinate of the connected component of the element a in the binarization matrix corresponding to the remaining pixel points by using the preset algorithm.

The first receiving module 406 is configured to receive a positioning algorithm selection instruction input by the user through the positioning algorithm selection interface.

The first setting module 407 is configured to set the algorithm for selecting the positioning algorithm selection instruction to the preset algorithm in response to the positioning algorithm selection instruction.

The second receiving module 408 is configured to receive a threshold setting instruction input by the user before the obtaining module obtains a matrix of luminance values of each pixel of the target image, where the threshold setting instruction carries a threshold.

The second setting module 409 is configured to set the threshold carried by the threshold setting instruction to a first threshold, a second threshold, a third threshold, and/or a fourth threshold in response to the threshold setting instruction.

Please refer to FIG. 6. FIG. 6 is a schematic structural diagram of a single molecule positioning device according to an embodiment of the present invention. As shown in FIG. 6, the single molecule positioning device includes a processor 601, a memory 602, an output device 603, an input device 604, and a bus 605. As shown in FIG. 6, memory 602, output device 603, and input device 604 are coupled to processor 601 via bus 605. The memory 602 stores a set of program codes, and the processor 601 is configured to invoke the program code stored in the memory 602 to perform the following operations:

Obtaining a matrix of luminance values of each pixel of the target image, where the matrix of luminance values is a matrix having pixel values of preset pixels and preset pixel numbers centered on the luminance values of the pixel points;

Comparing the brightness value matrix with the preset matrix, and removing the pixel points corresponding to the brightness value matrix whose similarity is less than the first threshold;

The remaining pixels are positioned to achieve single molecule positioning.

As an optional implementation manner, the processor 601 compares the luminance value matrix with the preset matrix, and removes the pixel points corresponding to the luminance value matrix whose similarity is less than the first threshold.

Calculating a similarity value between each luminance value matrix and a preset matrix to obtain a similarity value matrix;

Comparing each element in the similarity value matrix with the size of the first threshold, removing pixel points corresponding to the elements of the similarity value matrix that are smaller than the first threshold.

As an optional implementation manner, the processor 601 further performs the following steps:

And removing a pixel corresponding to the element of the similarity value matrix that is greater than the third threshold, the third threshold being greater than the first threshold.

As an optional implementation manner, the processor 601 compares the size of each element in the similarity value matrix with the first threshold, and removes the pixel corresponding to the element of the similarity value matrix that is smaller than the first threshold.

Comparing the size of each element in the similarity value matrix with the first threshold;

Assigning an element of the similarity value matrix that is greater than or equal to the first threshold to a, and assigning an element of the similarity value matrix that is smaller than the first threshold to b, to obtain a binarized matrix, in the binarization matrix The element is selected from one of a and b, a is not equal to b;

As an optional implementation manner, the processor 601 performs the following steps before or after removing all the pixel points corresponding to the binarization matrix of the element b:

Determining a connected component of the element a in the binarization matrix;

As an optional implementation manner, after the processor 601 determines the connected component of the element a in the binarization matrix, the following steps may also be performed:

As an optional implementation manner, the manner in which the processor 601 locates the remaining pixel points is specifically:

The center coordinates of the connected components of the elements a in the binarization matrix corresponding to the remaining pixel points are determined by a preset algorithm to determine the coordinates of the single molecules.

As an optional implementation manner, the processor 601 may perform the following steps before determining, by using a preset algorithm, the center coordinates of the connected component of the element a in the binarization matrix corresponding to the remaining pixel points:

Outputting a positioning algorithm selection interface through the output device 603;

The algorithm for selecting the positioning algorithm selection instruction is set as the preset algorithm in response to the positioning algorithm selection instruction.

As an optional implementation manner, the processor 601 may perform the following steps before obtaining the matrix of the luminance values of each pixel of the target image:

Receiving, by the input device 604, a threshold setting instruction input by the user, the threshold setting instruction carrying a threshold;

The threshold value carried by the threshold setting instruction is set to a first threshold, a second threshold, a third threshold, and/or a fourth threshold in response to the threshold setting instruction.

Embodiments of the present invention also provide a system including a processor, a memory, an output device, an input device, and a bus. The memory, output device and input device are connected to the processor via a bus. A set of program code is stored in the memory, and the processor is configured to call the program code stored in the memory, and executable The operations performed by the processor 601.

It should be noted that, in the above embodiments, the descriptions of the various embodiments are different, and the parts that are not described in detail in a certain embodiment may be referred to the related descriptions of other embodiments. In addition, those skilled in the art should also understand that the embodiments described in the specification are all preferred embodiments, and the actions and modules involved are not necessarily required by the present invention.

The steps in the method of the embodiment of the present invention may be sequentially adjusted, merged, and deleted according to actual needs.

The modules or units in the single molecule positioning device of the embodiment of the invention can be combined, divided and deleted according to actual needs.

A person of ordinary skill in the art may understand that all or part of the steps of the foregoing embodiments may be completed by a program to instruct terminal device related hardware, and the program may be stored in a computer readable storage medium, and the storage medium may be Including: flash disk, read-only memory (ROM), random access memory (RAM), disk or optical disk.

The single molecule positioning method and device disclosed in the embodiments of the present invention are described in detail. The principles and embodiments of the present invention are described in the following. The description of the above embodiments is only for helping to understand the present invention. The method and its core idea; at the same time, those skilled in the art, according to the idea of the present invention, there will be changes in the specific implementation and application scope. In summary, the content of the specification should not be understood as Limitations of the invention.

Claims

A single molecule positioning method, comprising:

Obtaining a matrix of luminance values of each pixel of the target image, wherein the matrix of luminance values is a matrix having a preset number of rows and a pixel value of the preset number of columns, centered on the luminance value of the pixel;

Comparing the brightness value matrix with the preset matrix, and removing pixel points corresponding to the brightness value matrix whose similarity is less than the first threshold;

The remaining pixels are positioned to achieve the single molecule positioning.
The method according to claim 1, wherein the comparing the luminance value matrix with the preset matrix, and removing pixel points corresponding to the luminance value matrix whose similarity is less than the first threshold, includes:

Calculating a similarity value of each of the brightness value matrix and the preset matrix to obtain a similarity value matrix;

Comparing each element of the similarity value matrix with a size of the first threshold, and removing a pixel point corresponding to an element of the similarity value matrix that is smaller than the first threshold.
The method according to claim 2, wherein the method further comprises: removing pixel points corresponding to the elements of the similarity value matrix that are greater than the third threshold, the third threshold being greater than the first threshold.
The method according to claim 2, wherein each element of the comparison similarity value matrix and the size of the first threshold are removed, and an element of the similarity value matrix that is smaller than the first threshold is removed. Pixels, including:

Comparing the size of each element in the similarity value matrix with a first threshold;

Assigning an element of the similarity value matrix that is greater than or equal to the first threshold to a, and assigning an element of the similarity value matrix that is smaller than the first threshold to b, to obtain a binary value a matrix, the elements in the binarization matrix being selected from one of the a and the b, the a is not equal to the b;

The pixel points corresponding to the element b in the binarization matrix are removed.
Method according to claim 4, characterized in that elements in the binarization matrix are removed Before or after the corresponding pixel point of b, including:

Determining a connected component of the element a in the binarization matrix;

The pixel points corresponding to all the elements in the connected component whose element a is smaller than the second threshold are removed.
The method according to claim 5, wherein after the determining the connected component of the element a in the binarization matrix, the method further comprises:

The pixel point corresponding to all the elements in the connected component whose element a is greater than the fourth threshold is removed, and the fourth threshold is greater than the second threshold.
The method according to any one of claims 4 to 6, wherein the positioning of the remaining pixels includes:

Determining, by a preset algorithm, a center coordinate of a connected component of the element a in the binarization matrix corresponding to the remaining pixel points to determine coordinates of the single molecule.
The method according to claim 7, wherein the predetermined algorithm is selected from at least one of a centroid method, a Gaussian fitting method, a maximum likelihood method, a solution linear equation method, and a Ma Liang algorithm.
The method according to claim 7, wherein the predetermined algorithm is at least one of a centroid method and a Gaussian fitting method.
The method according to any one of claims 7 to 9, before the determining, by the preset algorithm, the center coordinates of the connected component of the element a in the binarization matrix corresponding to the remaining pixel points, the method further includes:

Output positioning algorithm selection interface;

Receiving a positioning algorithm selection instruction input by the user through the positioning algorithm selection interface;

And in response to the positioning algorithm selection instruction, setting an algorithm selected by the positioning algorithm selection instruction as a preset algorithm.
Method according to any one of claims 1 to 10, characterized in that Before the matrix of luminance values of each pixel of the target image, the method further includes:

Receiving a threshold input instruction input by a user, the threshold setting instruction carrying a threshold;

The threshold carried by the threshold setting instruction is set to a first threshold, a second threshold, a third threshold, and/or a fourth threshold in response to the threshold setting instruction.
A single molecule positioning device, characterized in that the single molecule positioning device comprises:

An obtaining module, configured to obtain a matrix of luminance values of each pixel of the target image, where the matrix of luminance values is a pixel value having a preset number of rows and a preset number of columns centered on a luminance value of the pixel Matrix

a removing module, configured to compare the brightness value matrix with a preset matrix, and remove pixel points corresponding to the brightness value matrix whose similarity is less than the first threshold;

a positioning module for positioning the remaining pixels to achieve the single molecule positioning.
The single molecule positioning device according to claim 12, wherein the removing module comprises:

a calculating unit, configured to calculate a similarity value of each of the brightness value matrix and the preset matrix, to obtain a similarity value matrix;

a comparing unit, configured to compare a size of each element of the similarity value matrix with the first threshold, and remove a pixel point corresponding to an element of the similarity value matrix that is smaller than the first threshold.
The single-molecular locating device according to claim 13, wherein the comparing unit is further configured to remove a pixel point corresponding to an element of the similarity value matrix that is greater than a third threshold, wherein the third threshold is greater than the The first threshold.
The single molecule positioning device according to claim 13, wherein the comparing unit compares each element in the similarity value matrix with a size of the first threshold, and removes the similarity value matrix from the first The manner in which the elements of the threshold correspond to the pixel points is specifically as follows:

Comparing the size of each element in the similarity value matrix with a first threshold;

Assigning an element of the element of the similarity value matrix that is greater than or equal to the first threshold to a, Assigning, among the elements of the similarity value matrix, an element smaller than the first threshold to b, to obtain a binarization matrix, the elements in the binarization matrix being selected from one of the a and the b , the a is not equal to the b;

The pixel points corresponding to the element b in the binarization matrix are removed.
The single molecule positioning device according to claim 15, wherein the single molecule positioning device further comprises:

a determining module, configured to determine a connected component of the element a in the binarization matrix before or after the comparing unit removes a pixel point corresponding to the element b in the binarization matrix;

The removing module is further configured to remove pixel points corresponding to all elements in the connected component whose number of elements a is less than a second threshold.
The single molecule positioning device according to claim 16, wherein the removing module is further configured to remove pixel points corresponding to all elements in the connected component whose number of elements a is greater than a fourth threshold, the fourth The threshold is greater than the second threshold.
The single molecule positioning device according to any one of claims 15 to 17, wherein the positioning module is specifically configured to:

Determining, by a preset algorithm, a center coordinate of a connected component of the element a in the binarization matrix corresponding to the remaining pixel points to determine coordinates of the single molecule.
The single molecule positioning device according to claim 18, wherein the preset algorithm is selected from at least one of a centroid method, a Gaussian fitting method, a maximum likelihood method, a solution linear equation method, and a Ma Liang algorithm.
The single molecule positioning device according to claim 18, wherein the preset algorithm is at least one of a centroid method and a Gaussian fitting method.
The single molecule positioning device according to any one of claims 18 to 20, characterized in that The single molecule positioning device further includes:

An output module, configured to output a positioning algorithm selection interface before the positioning module determines a center coordinate of a connected component of the element a in the binarization matrix corresponding to the remaining pixel points by using a preset algorithm;

a first receiving module, configured to receive a positioning algorithm selection instruction input by the user through the positioning algorithm selection interface;

The first setting module is configured to set, according to the positioning algorithm selection instruction, an algorithm selected by the positioning algorithm selection instruction as a preset algorithm.
The single molecule positioning device according to any one of claims 12 to 21, wherein the single molecule positioning device further comprises:

a second receiving module, configured to receive, after the obtaining module obtains a matrix of luminance values of each pixel of the target image, a threshold setting instruction input by the user, where the threshold setting instruction carries a threshold;

And a second setting module, configured to set, according to the threshold setting instruction, a threshold carried by the threshold setting instruction as a first threshold, a second threshold, a third threshold, and/or a fourth threshold.
A single molecule positioning device comprising a processor and a memory, the memory being connected to the processor, wherein the memory stores a set of program codes, and the processor is configured to call the stored in the memory The program code executes the method according to any one of 1 to 11.
A single molecule positioning system, characterized in that the system comprises a processor and a memory, the memory being connected to the processor, wherein the memory stores a set of program codes, the processor is used for The method described in any one of 1 to 11 is executed by calling the program code stored in the memory.
A computer readable storage medium, the one or more programs comprising instructions that, when executed by the single molecule positioning device, cause the single molecule positioning device to perform any of claims 1-11 The method described.