CN106556614B - A method of root system spacial framework is quantified based on CT scan technology - Google Patents
A method of root system spacial framework is quantified based on CT scan technology Download PDFInfo
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Abstract
The invention discloses a kind of methods based on CT scan technology quantization root system spacial framework, include the following steps: sample acquisition, sample CT scan, data enhancing, selected threshold, image cutting and binaryzation, three-dimensional visualization, three-dimensional quantitative analysis.Beneficial effects of the present invention: it is sampled using professional sampling instrument, reduces the disturbance to in-situ root system；CT scan instrument is combined with professional three dimensional analysis software, using most suitable threshold segmentation method, realizes the three-dimensional quantitative analysis to root system of plant space structure.
Description
Technical field
The invention belongs to agricultural engineering technology fields, and in particular to one kind quantifies root system spatial network based on CT scan technology
The method of structure.
Background technique
Tradition measurement root system method mainly have nail-plate method, container method, glass wall and glass tube method, isotopic measurement,
Porous membrane method washes Gen Fa and WinRHIZO software combined techniques, and nondestructive determination Ground Penetrating Radar method at present.These methods
Generally existing problem is concentrated mainly on the destruction to in-situ root system, it is artificial caused by error is larger or the more low side of precision
Face.Currently, having become international and domestic forward position the most using the method for CT scan method in situ measurement root system shape of space structure
Method, but due to scanning cost, and it is sampled into the limitation of present aspect, this method is not widely applied.In the world, though
This right method has been applied, but the method for sampling is larger using hand digging method perturbation；It has delivered at home
In terms of article is concentrated mainly on the Threshold segmentation and three-dimensional visualization of root system, relies primarily on related scholar and pass through the method for programming
Processing, without a special software and a whole set of unified data processing method.In addition, at home still to the research of root system
The quantization of the spacial framework of root system of plant is not implemented；Or it is confined to two-dimentional quantitative analysis；In analysis software aspects master
Will by means of the open source softwares such as programming software or Image J, the three-dimensional software of the profession such as Avizo using less.
Summary of the invention
For above-mentioned technical problem in the related technology, the present invention proposes a kind of based on CT scan technology quantization root system space
The method of network structure, to solve the above problems.
To realize the above-mentioned technical purpose, the technical scheme of the present invention is realized as follows:
A method of root system spacial framework is quantified based on CT scan technology, is included the following steps:
S1, sample acquisition: pvc pipe is pressed into soil, entire pvc pipe is sealed and is blocked with PVC lid after taking out, obtained
Intact soil root；
S2, CT scan: sample is lain against into CT scan equipment and is scanned；
S3, data enhancing: the resulting image of CT scan is imported into Avizo software and is rebuild, and image is passed through
Two kinds of filters of Fourier filters FFT filter and Gaussian filter Gaussian filter eliminate image noise, enhancing
Picture quality；
S4, threshold method further comprise:
S4.1, using growth method in conjunction with Global thresholding, utilize the conjury stick in the segmentation plate of Avizo
The threshold value for choosing root system, then adjusts threshold range around this threshold value, until the root system packet for needing to study in the image of display
Containing inside；
S4.2, selection 3D options, it will show entire root system in display window, by the expansion in menu bar and invade
Erosion, the root system that continuous adjustment and improvement obtain more；
S5, image cutting and binaryzation: by Avizo cutting tool, chosen area rejects splitting for portion disturbances generation
Gap obtains the binary map of root system in soil using the threshold method of step S4；
S6, three-dimensional visualization: (volume rendering) and surface rendering are rendered by the volume of Avizo
(isosurface rendering), realizes the three-dimensional visualization of soil root；
S7, three-dimensional quantitative analysis further comprise:
S7.1, the volume of root system in soil is obtained by the volume fraction volume fraction of Avizo；And/or
S7.2, it obtains regarding each independent root system into an object as by auto skeleton module, it is each right to analyze
As total parameter of root system in parameter, and the entire sample of analysis.
Preferably, the pipe range of the pvc pipe is 50cm, internal diameter 10cm.
Preferably, in step S2, the parameter of CT scan equipment is voltage 140KV, electric current 200mA, sweep span
0.625mm。
Further, in step S6, video is made while realizing three-dimensional visualization.
Further, in step S7.2, the parameter for analyzing each object includes analyzing the position of each object, angle, matching
Digit, surface area, number of nodes, Node distribution, equivalent redius, length, line segment number, end node points, branch node number and independence
Node.
Further, in step S7.2, the total parameter for analyzing root system in entire sample includes analyzing root system in entire sample
Total volume, total length, total node number, total end node points, total score branch number of nodes, total isolated node, root quantity is average long
Degree, average equivalent radius, total length.
Beneficial effects of the present invention: it is sampled using professional sampling instrument, reduces the disturbance to in-situ root system；CT scan instrument
It combines with professional three dimensional analysis software, using most suitable threshold segmentation method, realizes to the three of root system of plant space structure
Tie up quantitative analysis.
Specific embodiment
It is clearly and completely described below with reference to the technical solution in the embodiment of the present invention, it is clear that described implementation
Example is only a part of the embodiment of the present invention, instead of all the embodiments.Based on the embodiments of the present invention, this field is common
Technical staff's every other embodiment obtained, shall fall within the protection scope of the present invention.
A kind of method based on CT scan technology quantization root system spacial framework according to embodiments of the present invention, packet
Include following steps:
S1, sample acquisition: pvc pipe is pressed into soil, entire pvc pipe is sealed and is blocked with PVC lid after taking out, obtained
Intact soil root, the pipe range of the pvc pipe are 50cm, internal diameter 10cm；
S2, CT scan: lying against CT scan equipment for sample and be scanned, and the parameter of CT scan equipment is voltage 140KV,
Electric current 200mA, sweep span 0.625mm；
S3, data enhancing: the resulting image of CT scan is imported into Avizo software and is rebuild, and image is passed through
Two kinds of filters of FFT filter and Gaussian filter eliminate image noise, enhance picture quality；
S4, threshold method:
S4.1, using growth method in conjunction with Global thresholding, utilize the conjury stick in the segmentation plate of Avizo
The threshold value for choosing root system, then adjusts threshold range around this threshold value, until the root system packet for needing to study in the image of display
Containing inside；
S4.2, selection 3D options, it will show entire root system in display window, by the expansion in menu bar and invade
Erosion, the root system that continuous adjustment and improvement obtain more；
S5, image cutting and binaryzation: by Avizo cutting tool, chosen area rejects splitting for portion disturbances generation
Gap obtains the binary map of root system in soil using the threshold method of step S4；
S6, three-dimensional visualization: pass through the volume rendering module volume rendering and surface rendering module of Avizo
Isosurface rendering realizes the three-dimensional visualization of soil root, makes video while realizing three-dimensional visualization；
S7, three-dimensional quantitative analysis:
S7.1, the volume of root system in soil is obtained by the volume fraction volume fraction of Avizo；And/or
S7.2, it obtains regarding each independent root system into an object as by auto skeleton module, it is each right to analyze
As total parameter of root system in parameter, and the entire sample of analysis, the parameter for analyzing each object includes analyzing the position of each object
Set, angle, ligancy, surface area, node (node) number, Node distribution, equivalent redius, length, line segment number, end node points,
Branch node number and isolated node, in step S7.2, the total parameter for analyzing root system in entire sample includes analyzing in entire sample
The total volume of root system, total length, total node number, total end node points, total score branch number of nodes, total isolated node, root quantity are put down
Equal length, average equivalent radius, total length.
The present invention acquires acquire in-situ root system in sample soil first, and sampling function substantially reduces disturbing in sampling process
Dynamic, the method combined using CT scan with Avizo software analyzes the spacial framework of root system of plant.Using in Avizo
The threshold method that Global thresholding is combined with growth method realizes the visualization of root system of plant spacial framework.And it combines soft
The skeletonization method of part realizes the three-dimensional quantitative analysis of root system of plant space structure, these quantized datas include plant roots coefficient
Amount, equivalent diameter, ligancy, pore throat quantity etc..
The foregoing is merely illustrative of the preferred embodiments of the present invention, is not intended to limit the invention, all in essence of the invention
Within mind and principle, any modification, equivalent replacement, improvement and so on be should all be included in the protection scope of the present invention.
Claims (6)
1. a kind of method based on CT scan technology quantization root system spacial framework, characterized by the following steps:
S1, sample acquisition: pvc pipe is pressed into soil, entire pvc pipe is sealed and is blocked with PVC lid after taking out, do not disturbed
Dynamic soil root；
S2, CT scan: sample is lain against into CT scan equipment and is scanned；
S3, data enhancing: the resulting image of CT scan is imported into Avizo software and is rebuild, and Fourier is passed through to image
Leaf filter and Gaussian filter eliminate image noise, enhance picture quality；
S4, threshold method further comprise:
S4.1, using growth method in conjunction with Global thresholding, utilize conjury stick in the Segmentation plate of Avizo to choose
Then the threshold value of root system adjusts threshold range around this threshold value, until the root system in the image of display comprising needing to study；
S4.2, selection 3D options, it will entire root system is shown in display window, by the expansion and erosion in menu bar, no
The root system that disconnected adjustment and improvement obtain more；
S5, image cutting and binaryzation: by Avizo cutting tool, chosen area rejects the crack that portion disturbances generate, benefit
With the threshold method of step S4, the binary map of root system in soil is obtained；
S6, three-dimensional visualization: by the volume rendering of Avizo and surface rendering, the three-dimensional visualization of soil root is realized；
S7, three-dimensional quantitative analysis further comprise:
S7.1, the volume of root system in soil is obtained by the volume fraction of Avizo；And/or
S7.2, it obtains regarding each independent root system as an object by Auto skeleton module, analyzes each object ginseng
Total parameter of root system in number, and the entire sample of analysis.
2. the method based on CT scan technology quantization root system spacial framework, feature exist according to claim 1
In: the pipe range of the pvc pipe is 50cm, internal diameter 10cm.
3. the method based on CT scan technology quantization root system spacial framework, feature exist according to claim 1
In: in step S2, the parameter of CT scan equipment is voltage 140KV, electric current 200mA, sweep span 0.625mm.
4. the method based on CT scan technology quantization root system spacial framework, feature exist according to claim 1
In: in step S6, video is made while realizing three-dimensional visualization.
5. the method based on CT scan technology quantization root system spacial framework, feature exist according to claim 1
In: in step S7.2, the parameter for analyzing each object includes analyzing the position of each object, angle, ligancy, surface area, section
Points, Node distribution, equivalent redius, length, line segment number, end node points, branch node number and isolated node.
6. the method according to claim 5 based on CT scan technology quantization root system spacial framework, it is characterised in that:
In step S7.2, the total parameter for analyzing root system in entire sample includes analyzing the total volume of root system in entire sample, total length, always
Number of nodes, total end node points, total score branch number of nodes, total isolated node, root quantity, average length, average equivalent radius, always
Length.
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Families Citing this family (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN107945278A (en) * | 2017-12-14 | 2018-04-20 | 桂林电子科技大学 | The three-dimensionalreconstruction and finite element method of a kind of organism structure |
| CN108844979A (en) * | 2018-06-22 | 2018-11-20 | 西南大学 | A method of CT scan detection soil and root structure based on liftable fixture |
| CN109829941B (en) * | 2019-01-04 | 2021-02-19 | 华南农业大学 | Plant root system three-dimensional configuration measuring method based on centerline extraction |
| CN113390905B (en) * | 2021-05-31 | 2022-06-24 | 北京师范大学 | Method for quantifying pore space structure of soil aggregate based on CT scanning technology |
| CN116309560B (en) * | 2023-05-17 | 2023-08-08 | 北京师范大学 | Method and system for detecting moisture distribution of plant catheter |
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