Seed radicle growth modeling method based on three-dimensional image

Abstract

The invention relates to a seed radicle growth modeling method based on a three-dimensional image, and the method comprises the steps: scanning the structure and contour of a seed in a container through a tomography technology, and obtaining the three-dimensional image data of the seed and soil around the seed; then three-dimensional image data obtained through scanning are imported into computer software to obtain an original image, and the original image is reconstructed to obtain three-dimensional model data of the seeds and radicles of the seeds; constructing a seed model and a radicle model with a continuous annular structure according to the obtained three-dimensional model data of the seeds and radicles of the seeds; and finally, continuously scanning the seeds and radicles thereof in a growth cycle, and endowing each annular structure in the radicle model with a motion attribute according to the growth condition of the radicles, so as to construct a growth model of the seeds and radicles thereof to simulate the growth condition of the radicles. According to the seed radicle growth modeling method disclosed by the invention, the seed radicle model can be constructed for analog simulation on the premise of not damaging a seed growth environment, so that the scientificity is greatly improved.

Description

Technical Field

[0001] The invention relates to the technical field of three-dimensional modeling of crops, and in particular to a seed radicle growth modeling method based on three-dimensional images. Background Art

[0002] Corn is one of the three major grain crops in my country and has important economic value. However, since it is a seed with cotyledons remaining in the soil, traditional observation methods make it difficult to observe its root growth without destroying the soil. In addition, most traditional measurement methods are destructive detection, which makes it difficult to ensure the continuity of the experiment.

[0003] With the emergence of non-destructive testing such as computed tomography, compared with traditional destructive testing, computed tomography has many advantages. The tomographic images it generates can clearly show the connection between objects with large density differences, such as the relationship between seed radicles and soil. It can also provide more detailed three-dimensional data to help us better understand the morphology and structure of seed radicles when growing in the soil. It can also be measured continuously during crop growth without destroying the seed growth environment, greatly ensuring the continuity of the experiment. Based on the three-dimensional tomographic images it provides, the model is constructed using the method of coaxial stacking growth of radicles. Therefore, the tomographic images presented by computed tomography provide a very effective method for modeling seed radicle growth.

[0004] Currently there is no method to model seed radicle growth using computed tomography. Summary of the invention

[0005] The purpose of the present invention is to overcome the shortcomings of the prior art and provide a seed radicle growth modeling method based on three-dimensional images. The seed radicle growth modeling method can construct a seed radicle model for simulation without destroying the seed growth environment, thereby greatly improving the scientificity.

[0006] The technical solution of the present invention to solve the above technical problems is:

[0007] A seed radicle growth modeling method based on three-dimensional images comprises the following steps:

[0008] S1: Use tomography technology to scan the structure and contour of the seeds in the container to obtain three-dimensional image data of the seeds and the surrounding soil;

[0009] S2: importing the scanned three-dimensional image data into computer software to obtain an original image, and reconstructing the original image to obtain three-dimensional model data of the seed and its radicle;

[0010] S3: constructing a seed model and a radicle model with a continuous ring structure according to the obtained three-dimensional model data of the seed and its radicle;

[0011] S4: Continuously scan the seeds and their radicles during the growth cycle, and assign motion properties to each ring structure in the radicle model according to the growth of the radicle, so as to construct a growth model of the seeds and their radicles to simulate the growth of the radicle.

[0012] Preferably, in step S1, the structure and contour of the seeds in the container are scanned using a three-dimensional X-ray emitted by a computer tomography scanner to obtain three-dimensional image data of the seeds and the surrounding soil; the specific steps are:

[0013] S101: planting seeds in a container, and fixing the container on a sample stage of an electronic computer tomography scanner;

[0014] S102: Select a scanning mode, set various parameters of the CT scanner, and set the slice interval according to the required observation accuracy, use the CT scanner to scan the soil and seeds, and obtain all slice images of the seeds and their radicles.

[0015] Preferably, in step S102, the scanning mode includes eccentric rotation and concentric rotation.

[0016] Preferably, in step S102, the parameters of the electronic computer tomography scanner include voltage, current, rotation step distance and number of shots.

[0017] Preferably, in step S2, when reconstructing the original image, the original image needs to be processed, which specifically includes the following steps:

[0018] S201: Segmenting the seeds and their radicles using software tools according to their density ranges, separating the seeds and their radicles from the soil and the carrier, and forming a three-dimensional structure image;

[0019] S202: extracting various physical parameters of the seeds and their radicles, wherein the physical parameters include seed burial depth, radicle length, diameter data, relative position coordinates and relative density.

[0020] Preferably, the three-dimensional structure image includes a grayscale image and a color image.

[0021] Preferably, in step S3, the steps of constructing the radicle model are:

[0022] S301: According to the radicle diameter data obtained in step S202, the radicle diameter data meeting the requirements are arranged in order from large to small, and marked with serial numbers;

[0023] S302: Use simulation software to make a radicle ring structure. According to the arranged diameter data, a series of radicle ring structures are made. The ring structure with the largest diameter is connected to the seed, and the ring structure with the smallest diameter is used as the tail. Finally, all the ring structures are stacked in the same plane and embedded into the seed model.

[0024] Preferably, in step S4, the specific steps of constructing the growth model of seeds and their radicles are:

[0025] S401: during the growth period of seed rooting, repeating steps S1 and S2 at regular intervals to obtain growth data of seed radicles at different periods;

[0026] S402: constructing a coordinate system with the connection between the radicle and the seed as the origin, extracting the spatial coordinate points of the radicle tip from the three-dimensional image of each time period to calculate the average value of the spatial coordinate points of the dynamic growth of the radicle tip, so as to obtain the average trajectory of the dynamic growth of the radicle, and according to the average trajectory, respectively and sequentially assigning movement behaviors starting at different times to each radicle ring structure;

[0027] S403: All the radicle ring structures are moved in sequence from the end of the radicle with the smallest diameter to the root of the radicle with the largest diameter at specific speeds and directions, thereby ultimately simulating the dynamic process of seed radicle growth.

[0028] Preferably, in step S4, after the growth model of the seed and its radicle is constructed, it is necessary to verify the accuracy and reliability of the growth model of the seed and its radicle, and the specific steps are:

[0029] The seeds and their radicles are taken out of the soil, and the excess surface soil is cleaned. The growth length and growth direction of the radicles are measured and compared with the output results in the growth model of the seeds and their radicles, and it is determined whether the error between the two is within the allowable range of accuracy, so as to evaluate the accuracy and reliability of the growth model of the seeds and their radicles; when the error between the two is not within the allowable range of accuracy, the growth model of the seeds and their radicles needs to be adjusted and corrected until the accuracy and reliability of the growth model of the seeds and their radicles meet the accuracy requirements.

[0030] Preferably, in step S402, the movement behavior includes displacement and rotation along the average trajectory.

[0031] Compared with the prior art, the present invention has the following beneficial effects:

[0032] 1. The seed radicle growth modeling method based on three-dimensional images of the present invention adopts a non-destructive detection method such as tomography technology, which can extract the tomographic three-dimensional image data of the seed radicle at a specified interval in the soil. According to the tomographic three-dimensional image data, a method of coaxial stacking growth of radicles is adopted to construct a growth model of seeds and their radicles. In this way, the growth model of seeds and their radicles can be constructed for simulation without destroying the growth environment of the seeds, thereby greatly improving the scientificity.

[0033] 2. The seed radicle growth modeling method based on three-dimensional images of the present invention uses a non-destructive testing method, which can continuously obtain the physical parameters of the seeds and their radicles and their positions in the soil, which can greatly improve the detection efficiency and quality, and can observe the growth process of the same seed in the soil throughout the whole process, greatly reducing the experimental deviation caused by individual differences.

[0034] 3. The seed and radicle growth model constructed by the present invention constructs multiple ring structures of the radicle through three-dimensional image data, and gives each ring structure of the radicle a different movement state according to the actual growth situation, thereby ensuring the accuracy of the simulation process. BRIEF DESCRIPTION OF THE DRAWINGS

[0035] Figure 1 It is a schematic diagram of the process of the seed radicle growth modeling method based on three-dimensional images of the present invention.

[0036] Figure 2 Schematic diagram of the structure of the growth model of seeds and their radicle.

[0037] Figure 3 Schematic diagram of the structure of the radicle model.

[0038] Figure 4 A three-dimensional image of a seed radicle in soil using computed tomography. DETAILED DESCRIPTION

[0039] The present invention is further described in detail below in conjunction with embodiments and drawings, but the embodiments of the present invention are not limited thereto.

[0040] See also Figure 1-Figure 4 The seed radicle growth modeling method based on three-dimensional images of the present invention comprises the following steps:

[0041] S1: Use tomography technology to scan the structure and contour of the seeds in the container to obtain three-dimensional image data of the seeds and the surrounding soil;

[0042] In this embodiment, the structure and contour of the seeds in the container are scanned using three-dimensional X-rays emitted by a computer tomography scanner to obtain three-dimensional image data of the seeds and the surrounding soil; the specific steps are:

[0043] S101: planting seeds in a container, and fixing the container on a sample stage of an electronic computer tomography scanner;

[0044] S102: According to actual conditions, a scanning mode is selected, wherein the scanning mode includes eccentric rotation scanning and concentric rotation scanning; various parameters of the electronic computer tomography scanner are set, wherein the various parameters of the electronic computer tomography scanner include voltage, current, rotation step distance, and number of shots; and the tomography interval is set according to the required observation accuracy, and the soil and seeds are scanned using the electronic computer tomography scanner to ensure that the soil around the seeds and their radicles (including the top, bottom, and sides) is covered, and finally all tomographic images of the seeds and their radicles are obtained.

[0045] S2: Import the scanned three-dimensional image data into computer software to obtain the original image, and reconstruct the original image to obtain the three-dimensional model data of the seed and its radicle, so as to fully and clearly present the three-dimensional structure of the entire seed and the radicle, and use the supporting software to fully display the three-dimensional spatial distribution of the seed and the radicle in the soil;

[0046] In the above process, the original image data needs to be processed to remove interference items and irrelevant parts in the soil to obtain accurate three-dimensional model data of seeds and their radicles, which specifically includes the following steps:

[0047] S201: Segmenting the seeds and their radicles using software tools according to their density ranges, separating the seeds and their radicles from the soil and the carrier, and forming a three-dimensional structure image, wherein the three-dimensional structure image includes a grayscale image and a color image;

[0048] S202: extracting various physical parameters of the seeds and their radicles, wherein the physical parameters include seed burial depth, radicle length, diameter data, relative position coordinates and relative density.

[0049] In addition, the three-dimensional image data are X-ray images collected from different angles. In order to reconstruct these three-dimensional image data into three-dimensional images, it is necessary to use the mathematical method of tomographic reconstruction, which generally adopts the back projection method and the filtered back projection method. Among them, the former is to reversely project each three-dimensional image data along the original acquisition direction, and accumulate these projections to obtain a preliminary reconstructed image; and the mathematical principle of back projection is to use the projection theorem to inverse transform the two-dimensional projection data back to three-dimensional space. Therefore, the latter is an improvement on the basic back projection method. It first applies a filter (usually a Ranchos filter or a Hanning filter) to each three-dimensional image data to enhance the edges and details of the image, and then performs back projection. Among them, the purpose of filtering is to eliminate the blurring effect produced in the back projection process, thereby improving the clarity of the reconstructed image; the supporting computer software uses these two methods for reconstruction and completes it automatically.

[0050] S3: constructing a seed model and a radicle model with a continuous ring structure according to the obtained three-dimensional model data of the seed and its radicle; wherein the steps of constructing the radicle model are as follows:

[0051] S301: According to the radicle diameter data obtained in step S202, the radicle diameter data meeting the requirements are arranged in order from large to small, and marked with serial numbers;

[0052] S302: Use simulation software to make a radicle ring structure. According to the arranged diameter data, a series of radicle ring structures are made. The ring structure with the largest diameter is connected to the seed, and the ring structure with the smallest diameter is used as the tail. Finally, all the ring structures are stacked in the same plane and embedded into the seed model.

[0053] In this embodiment, the principle of radicle modeling is to generate a series of annular structures through simulation software, which are arranged from large to small according to diameter, and then stacked on the same plane and embedded in the seed model. This process is based on accurate three-dimensional model data obtained from three-dimensional X-ray scanning and data reconstruction, which is used to simulate the growth and structure of the radicle; after data reconstruction, the diameter data of each annular structure is extracted and input (for example, the initial length of each annular structure is 0.1mm, but the diameter of the annular structure is 0.5mm, 1mm, 2mm, 1.3mm, 2.4mm, etc.), which determines the size and arrangement order of the annular structure. A series of annular structures are generated using these data. According to the preset arrangement rules and logic, these annular structures are arranged in order; since the annular structures of the radicle are usually arranged in a certain order in nature, stacking them on the same plane can better simulate this natural arrangement. In addition, this arrangement method can also increase the stability of the entire structure and avoid morphological instability caused by the dispersion of the annular structure. In addition, embedding the annular structure into the seed model can facilitate subsequent growth simulation and analysis to ensure the consistency and integrity of the model. In addition, the purpose of this design principle is to restore the natural growth process of the radicle as much as possible and provide a stable and accurate model for the next step of assigned growth research.

[0054] S4: Continuously scan the seeds and their radicles during the growth cycle, and assign motion attributes to each ring structure in the radicle model according to the growth of the radicle, so as to construct a growth model of the seeds and their radicles to simulate the growth of the radicle;

[0055] In this embodiment, the specific steps of constructing the growth model of seeds and their radicles are:

[0056] S401: during the growth period of seed rooting, repeating steps S1 and S2 at regular intervals to obtain growth data of seed radicles at different periods;

[0057] S402: constructing a coordinate system with the connection between the radicle and the seed as the origin, extracting the spatial coordinate points of the radicle tip from the three-dimensional image of each time period to calculate the average value of the spatial coordinate points of the dynamic growth of the radicle tip, so as to obtain the average trajectory of the dynamic growth of the radicle, and according to the average trajectory, respectively and sequentially assigning motion behaviors starting at different times to each radicle ring structure, wherein the motion behaviors include displacement and rotation along the average trajectory;

[0058] S403: moving all the radicle ring structures in sequence from the end of the radicle with the smallest diameter to the root of the radicle with the largest diameter at specific speeds and directions, thereby ultimately simulating the dynamic process of seed radicle growth;

[0059] In this embodiment, the assigned speed is calculated based on the average growth rate of the tip of the radicle within the time period of radicle growth. The specific method is: calculate the displacement of the tip of the radicle in each time period, and take the average value of the displacement in each time period as the elongation speed of the annular structure; that is, speed = ∑ (displacement) / number of time periods; and the assigned direction is determined based on the change direction of the spatial coordinate point of the tip of the radicle. The specific method is: calculate the spatial coordinate change vector of the tip of the radicle in each time period, and take the average value of the change vector in each time period as the translation or rotation direction of the annular structure, that is, direction = ∑ (change vector) / number of time periods.

[0060] S405: After the growth model of the seed and its radicle is constructed, the accuracy and reliability of the growth model of the seed and its radicle need to be verified. The specific steps are:

[0061] The seeds and their radicles are taken out of the soil, and the excess surface soil is cleaned. The growth length and growth direction of the radicles are measured and compared with the output results in the growth model of the seeds and their radicles, and it is determined whether the error between the two is within the allowable range of accuracy, so as to evaluate the accuracy and reliability of the growth model of the seeds and their radicles; when the error between the two is not within the allowable range of accuracy, the growth model of the seeds and their radicles needs to be adjusted and corrected until the accuracy and reliability of the growth model of the seeds and their radicles meet the accuracy requirements.

[0062] In this embodiment, after the growth model of the seed and its radicle is built, the growth of the seed root system can be calculated through the following data: (1) spatial coordinate data, the three-dimensional spatial coordinate data of the radicle tip at different time points obtained by repeated scanning; (2) growth length, by calculating the change of the radicle tip position, the growth length of the radicle in each time period is obtained; (3) growth rate: according to the growth length and time interval, the growth rate of the radicle in different growth periods is calculated; (4) growth direction: by analyzing the change direction of the radicle tip position, the growth direction of the radicle is obtained; (5) physical parameters: such as radicle diameter, seed burial depth, relative density, etc., through the above data, the growth morphology and structural changes of the radicle can be further analyzed. Through the comprehensive analysis of the above data, the growth of the seed root system can be fully calculated and evaluated, and the dynamic process and law of radicle growth can be obtained.

[0063] The above is a preferred embodiment of the present invention, but the embodiment of the present invention is not limited to the above content. Any other changes, modifications, substitutions, combinations, and simplifications that do not deviate from the spirit and principles of the present invention should be equivalent replacement methods and are included in the protection scope of the present invention.

Claims

1. A seed radicle growth modeling method based on three-dimensional images, characterized in that: The following steps are involved: S1: Use tomography technology to scan the structure and contour of the seeds in the container to obtain three-dimensional image data of the seeds and the surrounding soil; S2: importing the scanned three-dimensional image data into computer software to obtain an original image, and reconstructing the original image to obtain three-dimensional model data of the seed and its radicle; S3: constructing a seed model and a radicle model with a continuous ring structure according to the obtained three-dimensional model data of the seed and its radicle; S4: Continuously scan the seeds and their radicles during the growth cycle, and assign motion properties to each ring structure in the radicle model according to the growth of the radicle, so as to construct a growth model of the seeds and their radicles to simulate the growth of the radicle.

2. The seed radicle growth modeling method based on three-dimensional images according to claim 1, characterized in that: In step S1, the structure and contour of the seeds in the container are scanned using a three-dimensional X-ray emitted by a computer tomography scanner to obtain three-dimensional image data of the seeds and the surrounding soil; the specific steps are: S101: planting seeds in a container, and fixing the container on a sample stage of an electronic computer tomography scanner; S102: Select a scanning mode, set various parameters of the CT scanner, and set the slice interval according to the required observation accuracy, use the CT scanner to scan the soil and seeds, and obtain all slice images of the seeds and their radicles.

3. The seed radicle growth modeling method based on three-dimensional images according to claim 2, characterized in that: In step S102, the scanning mode includes eccentric rotation and concentric rotation.

4. The seed radicle growth modeling method based on three-dimensional images according to claim 2 is characterized in that: In step S102, various parameters of the CT scanner include voltage, current, rotation step distance, and number of images.

5. The seed radicle growth modeling method based on three-dimensional images according to claim 1, characterized in that: In step S2, when reconstructing the original image, the original image needs to be processed, which specifically includes the following steps: S201: Segmenting the seeds and their radicles using software tools according to their density ranges, separating the seeds and their radicles from the soil and the carrier, and forming a three-dimensional structure image; S202: extracting various physical parameters of the seeds and their radicles, wherein the physical parameters include seed burial depth, radicle length, diameter data, relative position coordinates and relative density.

6. The seed radicle growth modeling method based on three-dimensional images according to claim 5, characterized in that: The three-dimensional structure image includes a grayscale image and a color image.

7. The seed radicle growth modeling method based on three-dimensional images according to claim 5, characterized in that: In step S3, the steps of constructing the radicle model are: S301: According to the radicle diameter data obtained in step S202, the radicle diameter data meeting the requirements are arranged in order from large to small, and marked with serial numbers; S302: Use simulation software to make a radicle ring structure. According to the arranged diameter data, a series of radicle ring structures are made. The ring structure with the largest diameter is connected to the seed, and the ring structure with the smallest diameter is used as the tail. Finally, all the ring structures are stacked in the same plane and embedded into the seed model.

8. The seed radicle growth modeling method based on three-dimensional images according to claim 1, characterized in that: In step S4, the specific steps of constructing the growth model of seeds and their radicles are: S401: during the growth period of seed rooting, repeating steps S1 and S2 at regular intervals to obtain growth data of seed radicles at different periods; S402: constructing a coordinate system with the connection between the radicle and the seed as the origin, extracting the spatial coordinate points of the radicle tip from the three-dimensional image of each time period to calculate the average value of the spatial coordinate points of the dynamic growth of the radicle tip, so as to obtain the average trajectory of the dynamic growth of the radicle, and according to the average trajectory, respectively and sequentially assigning movement behaviors starting at different times to each radicle ring structure; S403: All the radicle ring structures are moved in sequence from the end of the radicle with the smallest diameter to the root of the radicle with the largest diameter at specific speeds and directions, thereby ultimately simulating the dynamic process of seed radicle growth.

9. The seed radicle growth modeling method based on three-dimensional images according to claim 8, characterized in that: In step S4, after the growth model of the seed and its radicle is constructed, the accuracy and reliability of the growth model of the seed and its radicle need to be verified. The specific steps are: The seeds and their radicles are taken out of the soil, and the excess surface soil is cleaned. The growth length and growth direction of the radicles are measured and compared with the output results in the growth model of the seeds and their radicles, and it is determined whether the error between the two is within the allowable range of accuracy, so as to evaluate the accuracy and reliability of the growth model of the seeds and their radicles; when the error between the two is not within the allowable range of accuracy, the growth model of the seeds and their radicles needs to be adjusted and corrected until the accuracy and reliability of the growth model of the seeds and their radicles meet the accuracy requirements.

10. The seed radicle growth modeling method based on three-dimensional images according to claim 8, characterized in that: In step S402, the movement behavior includes displacement and rotation along the average trajectory.

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