Method for measuring curvature of plant stem tip meristem based on Matlab

Abstract

The invention relates to the technical field of plant curvature, in particular to a method for measuring plant stem tip meristem curvature based on Matlab, which comprises the following steps: taking a photo of a stem tip meristem under a confocal microscope; identifying data points of all edges on the stem tip meristem on the basis of an edge identification algorithm according to the photo of the stem tip meristem, and obtaining a plurality of optimal points on the edges according to the positions of the data points in the photo; and fitting all the optimal points into a parabola, and calculating the plant stem tip meristem curvature. According to the method, input of a large amount of manpower is avoided, the method is objective, the edge of the stem tip meristem is detected through the Matlab edge recognition algorithm, and then fitting is conducted through the quadratic function.

Description

Technical Field

[0001] The invention relates to the technical field of plant curvature, and in particular to a method for measuring the curvature of plant stem apex meristem based on Matlab. Background Art

[0002] Certain scientific questions require observing changes in the curvature of the plant shoot apical meristem. The Kappa – Curvature Analysis (Kappa) plugin in Fiji Is Just ImageJ (Fiji) software allows you to manually outline the meristem margins and measure curvature after importing confocal microscopy images.

[0003] In the prior art, the Kappa plug-in requires manual selection of data points. These points are connected into straight lines in the order of selection, and a finite number of straight lines form a curve, which outlines the edge of the shoot apical meristem. However, in specific scientific research analysis, the Kappa plug-in still has many disadvantages. First, the number of these manually selected data points is limited, and they cannot perfectly fit the edge of the meristem; second, the manual selection of boundary points is subjective, and if a large number of images need to be selected for point analysis, there will be large errors; finally, if the curvature of a certain point on the curve needs to be measured instead of the average curvature, the selection of the data point closest to this point will have a greater impact on the curvature value. In summary, the Kappa plug-in can still be used for roughly measuring the curvature of the shoot apical meristem. But for precise measurement, we urgently need some new methods. Summary of the Invention

[0004] In order to overcome the shortcomings of the background technology, the present invention provides a method for measuring the curvature of plant stem apical meristem based on Matlab. The method avoids the input of a large amount of manpower and is an objective method. The edge of the stem apical meristem is first detected using Matlab's edge recognition algorithm, and then a quadratic function is used to fit it.

[0005] The first object of the present invention is to provide a method for measuring the curvature of plant stem apical meristem based on Matlab, comprising: Photographs of the shoot apical meristem were taken under a confocal microscope; Based on the edge recognition algorithm based on the photograph of the shoot apical meristem, all the data points on the edge of the shoot apical meristem are identified, and multiple optimal points on the edge are obtained according to the position of the data points in the image; All optimal points were fitted into parabolas to calculate the curvature of the plant shoot apical meristem.

[0006] Preferably, the edge recognition algorithm adopts the edge recognition zerocross algorithm.

[0007] Preferably, multiple optimal points on the edge are obtained according to the positions of the data points in the image, including: First, identify the coordinates of all edge data points on the shoot apical meristem in pixels: , where each Corresponding to multiple , each The corresponding array Select the data point corresponding to the smallest value; Then select the data points corresponding to the adjacent minimum values The data point with the minimum value is taken as the optimal point, and multiple optimal points are screened out in turn.

[0008] Preferably, in the process of screening the optimal point, all Arrange in ascending order, group the data points corresponding to the adjacent smallest values into a group, and find the The data point with the minimum value is selected, and the remaining data points in each group are deleted in turn, and the remaining data points are taken as the optimal points.

[0009] Preferably, all optimal points are fitted into a parabola to calculate the curvature of the plant stem apical meristem, including: fitting multiple optimal points into a parabola, and taking the curvature of the highest point of the parabola as the curvature of the stem apical meristem.

[0010] Preferably, a quadratic function is used Perform parabola fitting, the curvature at the highest point of the parabola is equal to .

[0011] A second object of the present invention is to provide a computer program product, comprising a computer program, which, when executed by a processor, implements a Matlab-based method for measuring the curvature of a plant stem apical meristem.

[0012] A third object of the present invention is to provide an electronic device comprising: processor; and a memory for storing executable instructions of the processor; The processor is configured to execute the Matlab-based method for measuring the curvature of plant stem apical meristem by executing the executable instructions.

[0013] A fourth object of the present invention is to provide a system for measuring the curvature of plant stem apical meristem based on Matlab, comprising: Image acquisition module, used to take pictures of the shoot apical meristem under a confocal microscope; An edge recognition module is used to identify all edge data points on the stem apical meristem based on a photograph of the stem apical meristem and an edge recognition algorithm, and obtain multiple optimal points on the edge based on the positions of the data points in the image; The curvature calculation module is used to fit all optimal points into parabolas and calculate the curvature of the plant stem apex meristem.

[0014] The present invention has at least the following beneficial effects: The present invention provides a Matlab-based method for measuring the curvature of plant stem apical meristems. Based on Matlab's edge recognition algorithm, the method identifies all edge data points on the stem apical meristem in pixels. By selecting the data point with the minimum value from each adjacent plurality of data points as the optimal point, this method provides sufficient data and avoids the subjectivity inherent in manual data point selection. The present invention utilizes a computer algorithm to identify the edges of the meristem, with a sufficient number of data points along the edges, to maximize the restoration of its shape. This method not only reduces human effort but also avoids the influence of subjective factors. BRIEF DESCRIPTION OF THE DRAWINGS

[0015] Figure 1 is a flow chart of the present invention; Figure 2 Detect the edges of the image using the zercross algorithm for edge detection; Figure 3 The edge points are obtained by taking the minimum value of all data points; Figure 4 is the minimum value point among multiple adjacent points (taking three adjacent points as an example); Figure 5 Comparison between the fitted quadratic function and the original image. DETAILED DESCRIPTION

[0016] In order to illustrate the technical means and effects adopted by the present invention to achieve the predetermined purpose of the invention, the following is a detailed description with reference to the embodiments.

[0017] The purpose of the present invention is to provide an objective method that can avoid a large amount of manpower input. The best choice is to first use Matlab's edge recognition algorithm to process the photos of the shoot apical meristem, then retain the optimal points of these data points, and finally use a quadratic function to fit them.

[0018] To achieve the above purpose, see Figure 1 As shown, the present invention provides a method for measuring the curvature of plant stem apical meristem based on Matlab, comprising: S1, photos of the shoot apical meristem taken under a confocal microscope; S2, based on the edge recognition algorithm, identifying all edge data points on the shoot apical meristem in pixels; See also Figure 2 As shown, the edge recognition algorithm uses the edge recognition zerocross algorithm.

[0019] S3. Obtain multiple optimal points on the edge according to the position of the data point in the image; The size of the tissue was calculated based on the actual distance represented by each optimal point pixel; It should be noted that in edge recognition, the upper left corner of the image is defined as the zero point. Among the data points with the same axis value, select the smallest one; that is, each There is only one value The value corresponds to it.

[0020] Obtain multiple optimal points on the edge based on the location of the data point in the image, including: See also Figure 3 As shown, first identify the coordinates of all edge data points on the shoot apical meristem in pixels as follows: , where each Corresponding to multiple , each The corresponding array Select the data point corresponding to the smallest value; Then select the data points corresponding to the adjacent minimum values The data point with the minimum value is taken as the optimal point, and multiple optimal points are screened out in turn.

[0021] See also Figure 4 As shown, in the process of screening the optimal point, all Arrange in ascending order, group the data points corresponding to the adjacent smallest values into a group, and find the The data point with the minimum value is selected, and the remaining data points in each group are deleted in turn, and the remaining data points are taken as the optimal points.

[0022] S4. Fit all optimal points into parabolas and calculate the curvature of the plant stem apical meristem.

[0023] Fit all optimal points to parabolas and calculate the curvature of the plant's shoot apex meristem, including: Multiple optimal points are fitted to calculate a parabola, and the curvature of the highest point of the parabola is taken as the curvature of the shoot apical meristem.

[0024] Using quadratic functions Perform parabola fitting, the curvature at the highest point of the parabola is equal to See also Figure 5As shown in Figure 2, the comparison between the fitted quadratic function and the original image is shown.

[0025] To this end, the present invention adopts the edge recognition algorithm based on Matlab to identify the data points of all edges on the stem apical meristem in pixels. After identification, for each Corresponding to multiple , then each The corresponding array Take the smallest value among them, which roughly filters out all the points on the edge. To further reduce the error, Arrange in ascending order, group each element into a group, and find the minimum data point in each group By deleting the remaining data points in the group, the remaining data points perfectly depict the edge of the shoot apical meristem. This method has a sufficient amount of data and also avoids the subjective problem of manually selecting data points.

[0026] In addition, using the quadratic function To fit these data points, the opening size of the parabola (i.e. the fitted The value of ) represents the curvature of the stem apical meristem, and the curvature at the highest point of the parabola (i.e. the highest point of the stem apical meristem) is equal to .

[0027] To illustrate the effect of microgravity on the morphological structure of plant stem apical meristems, the 0-1 cm bolting Arabidopsis thaliana stem apical meristems were placed on a three-dimensional random orientation rotator for 3 days, and 24 images of the Arabidopsis thaliana stem apical meristems were taken in the vertical direction using a confocal microscope. A total of 96 photos were obtained. After these photos were processed according to the method provided by the present invention, all of them were successfully fitted with a parabola close to the edge of the shoot apical meristem, and the curvature was calculated. Among them, the goodness of fit ( ) 84.38% were greater than 0.9, 97.91% were greater than 0.8, and 100% were greater than 0.7. This also indirectly reflects the rationale of using a parabola to fit the shoot apical meristem. Ultimately, it was found that growth in a microgravity environment had no effect on the curvature of the Arabidopsis shoot apical meristem.

[0028] The present invention provides a computer program product, comprising a computer program. When the computer program is executed by a processor, a Matlab-based method for measuring the curvature of a plant stem apex meristem is implemented.

[0029] The present invention provides an electronic device, comprising: processor; and a memory for storing executable instructions of the processor; The processor is configured to execute the Matlab-based method for measuring the curvature of plant stem apical meristem by executing the executable instructions.

[0030] The present invention provides a plant stem apex meristem curvature measurement system based on Matlab, comprising: An image acquisition module, used to obtain the shoot apical meristem; An edge recognition module is used to identify all edge data points on the stem apical meristem in units of pixels based on an edge recognition algorithm; select the data point with the minimum value from each plurality of adjacent data points as the optimal point, and sequentially select multiple optimal points; The curvature calculation module is used to perform parabolic fitting on multiple optimal points to obtain the curvature of the plant stem apex meristem.

[0031] The above description is only a preferred embodiment of the present invention and is not intended to limit the present invention. Any modifications, equivalent replacements, improvements, etc. made within the principles of the present invention should be included in the scope of protection of the present invention.

Claims

1. A method for measuring the curvature of plant stem apical meristem based on Matlab, characterized in that: include: Photographs of the shoot apical meristem were taken under a confocal microscope; Based on the edge recognition algorithm based on the photograph of the shoot apical meristem, all the data points on the edge of the shoot apical meristem are identified, and multiple optimal points on the edge are obtained according to the position of the data points in the image; All optimal points were fitted into parabolas to calculate the curvature of the plant shoot apical meristem.

2. the measuring method of the plant stem apex meristem curvature based on Matlab according to claim 1, is characterized in that, The edge recognition algorithm uses the edge recognition zerocross algorithm.

3. the measuring method of the plant stem apex meristem curvature based on Matlab according to claim 1, is characterized in that, Obtain multiple optimal points on the edge based on the location of the data point in the image, including: First, identify the coordinates of all edge data points on the shoot apical meristem in pixels: , where each Corresponding to multiple , each The corresponding array Select the data point corresponding to the smallest value; Then select the data points corresponding to the adjacent minimum values The data point with the minimum value is taken as the optimal point, and multiple optimal points are screened out in turn.

4. the measuring method of the plant stem apex meristem curvature based on Matlab according to claim 3, is characterized in that, In the process of screening the best point, all Arrange in ascending order, group the data points corresponding to the adjacent smallest values into a group, and find the The data point with the minimum value is selected, and the remaining data points in each group are deleted in turn, and the remaining data points are taken as the optimal points.

5. the measuring method of the plant stem apex meristem curvature based on Matlab according to claim 1, is characterized in that, Fitting all optimal points into a parabola to calculate the curvature of the plant stem apical meristem includes: fitting multiple optimal points into a parabola, and taking the curvature of the highest point of the parabola as the curvature of the stem apical meristem.

6. the measuring method of the plant stem apex meristem curvature based on Matlab according to claim 5, is characterized in that, Using quadratic functions Perform parabola fitting, the curvature at the highest point of the parabola is equal to .

7. A computer program product comprising a computer program, characterized in that When the computer program is executed by a processor, the Matlab-based method for measuring the curvature of plant stem apical meristem according to any one of claims 1 to 6 is implemented.

8. An electronic device, characterized in that: include: processor; as well as a memory for storing executable instructions of the processor; The processor is configured to execute the Matlab-based method for measuring the curvature of plant stem apical meristem according to any one of claims 1 to 6 by executing the executable instructions.

9. A Matlab-based system for measuring the curvature of plant stem apical meristems, characterized in that: include: Image acquisition module, used to take pictures of the shoot apical meristem under a confocal microscope; An edge recognition module is used to identify all edge data points on the stem apical meristem based on a photograph of the stem apical meristem and an edge recognition algorithm, and obtain multiple optimal points on the edge based on the positions of the data points in the image; The curvature calculation module is used to fit all optimal points into parabolas and calculate the curvature of the plant stem apex meristem.

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