CN106556614A - A kind of method that root system spacial framework is quantified based on CT scan technology - Google Patents
A kind of method that root system spacial framework is quantified based on CT scan technology Download PDFInfo
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- CN106556614A CN106556614A CN201610887431.3A CN201610887431A CN106556614A CN 106556614 A CN106556614 A CN 106556614A CN 201610887431 A CN201610887431 A CN 201610887431A CN 106556614 A CN106556614 A CN 106556614A
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N23/00—Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00
- G01N23/02—Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00 by transmitting the radiation through the material
- G01N23/04—Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00 by transmitting the radiation through the material and forming images of the material
- G01N23/046—Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00 by transmitting the radiation through the material and forming images of the material using tomography, e.g. computed tomography [CT]
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2223/00—Investigating materials by wave or particle radiation
- G01N2223/40—Imaging
- G01N2223/419—Imaging computed tomograph
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2223/00—Investigating materials by wave or particle radiation
- G01N2223/60—Specific applications or type of materials
- G01N2223/612—Specific applications or type of materials biological material
Abstract
The invention discloses a kind of method for quantifying root system spacial framework based on CT scan technology, comprises the steps：Sample collection, sample CT scan, data enhancing, selected threshold, image cutting and binaryzation, three-dimensional visualization, three-dimensional quantitative analysis.Beneficial effects of the present invention：Sampled using professional sampling instrument, reduce 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 field, and in particular to a kind of to quantify root system spatial network based on CT scan technology
The method of structure.
Background technology
Tradition determine root system method mainly have nail-plate method, container method, glass wall and glass tube method, isotopic measurement,
Porous membrane method, Gen Fa and WinRHIZO software combined techniqueses are washed, and nondestructive determination GPR method at present.These methods
Generally existing problem, is concentrated mainly on the destruction to in-situ root system, and the error for artificially causing is larger, or the more low side of precision
Face.At present, international and domestic forward position the most is had become using the method for CT scan method in site measurement root system shape of space structure
Method, but due to scanning cost, and the restriction of present aspect is sampled into, this method is not extensively applied.In the world, though
So this method has been applied, but the method for sampling is larger using hand digging method perturbation；Deliver at home
In terms of article is concentrated mainly on the Threshold segmentation and three-dimensional visualization of root system, method of the related scholar by programming is relied primarily on
Process, without a special software and a whole set of unified data processing method.In addition, at home to the research of root system still
The quantization of the spacial framework of unrealized root system of plant；Or it is confined to two-dimentional quantitative analysis；It is main in terms of analysis software
It is less by means of the use of the three-dimensional software of the specialty such as the open source software such as programming software or Image J, Avizo.
The content of the invention
For the above-mentioned technical problem in correlation technique, 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 above-mentioned technical purpose, the technical scheme is that what is be achieved in that：
A kind of method for quantifying root system spacial framework based on CT scan technology, comprises the steps：
S1, sample collection：Pvc pipe is pressed into into soil, whole pvc pipe is sealed and blocked with PVC lids after taking out, do not disturbed
Dynamic soil root；
S2, CT scan：Sample is lain against CT scan equipment to be scanned；
S3, data strengthen：Image obtained by CT scan is imported to and is rebuild in Avizo softwares, and Fourier is passed through to image
Two kinds of filters of leaf wave filter FFT filter and Gaussian filter Gaussian filter eliminate image noise, strengthen image
Quality；
S4, threshold method, further include：
S4.1, combined with Global thresholding using growth method, chosen using the conjury stick in the segmentation plates of Avizo
The threshold value of root system, then adjusts threshold range around this threshold value, until needing the root system studied to be included in the image for showing
It is interior；
S4.2, select 3D options, it will whole root system is shown in display window, by expansion and erosion in menu bar, no
Disconnected adjustment and the perfect root systems for obtaining more；
S5, image cutting and binaryzation：By Avizo cutting tools, chosen area, the crack that portion disturbances are produced, profit are rejected
With the threshold method of step S4, the binary map of root system in soil is obtained；
S6, three-dimensional visualization：Rendered by the volume of Avizo（volume rendering）And surface rendering（isosurface
rendering）, realize the three-dimensional visualization of soil root；
S7, three-dimensional quantitative analysis, further include：
S7.1, the volume that root system in soil is obtained by the volume fraction volume fraction of Avizo；And/or
S7.2, obtain regarding each independent root system as an object by auto skeleton modules, analyze each object and join
Number, and analyze total parameter of root system in whole sample.
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, realize making video while three-dimensional visualization.
Further, in step S7.2, the parameter for analyzing each object includes the position of each object of analysis, angle, matches somebody with somebody
Digit, surface area, 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 whole sample includes analyzing root system in whole sample
Cumulative volume, total length, total nodes, total end node points, total score nodes, total isolated node, root quantity are average long
Degree, average equivalent radius, total length.
Beneficial effects of the present invention：Sampled using professional sampling instrument, reduce the disturbance to in-situ root system；CT scan instrument
Combine with professional three dimensional analysis software, using most suitable threshold segmentation method, realize three to root system of plant space structure
Dimension quantitative analysis.
Specific embodiment
It is clearly and completely described with reference to the technical scheme in the embodiment of the present invention, it is clear that described enforcement
Example is only a part of embodiment of the invention, rather than the embodiment of whole.Based on the embodiment in the present invention, this area is common
The every other embodiment obtained by technical staff, belongs to the scope of protection of the invention.
A kind of described method for quantifying root system spacial framework based on CT scan technology, wraps according to embodiments of the present invention
Include following steps：
S1, sample collection：Pvc pipe is pressed into into soil, whole pvc pipe is sealed and blocked with PVC lids after taking out, do not disturbed
Dynamic soil root, the pipe range of the pvc pipe is 50cm, internal diameter 10cm；
S2, CT scan：Sample is lain against CT scan equipment to be scanned, the parameter of CT scan equipment is voltage 140KV, electric current
200mA, sweep span 0.625mm；
S3, data strengthen：Image obtained by CT scan is imported to and is rebuild in Avizo softwares, and FFT is passed through to image
Two kinds of filters of filter and Gaussian filter eliminate image noise, strengthen picture quality；
S4, threshold method：
S4.1, combined with Global thresholding using growth method, chosen using the conjury stick in the segmentation plates of Avizo
The threshold value of root system, then adjusts threshold range around this threshold value, until needing the root system studied to be included in the image for showing
It is interior；
S4.2, select 3D options, it will whole root system is shown in display window, by expansion and erosion in menu bar, no
Disconnected adjustment and the perfect root systems for obtaining more；
S5, image cutting and binaryzation：By Avizo cutting tools, chosen area, the crack that portion disturbances are produced, profit are rejected
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 module volume rendering and surface rendering module of Avizo
Isosurface rendering, realize the three-dimensional visualization of soil root, realize making video while three-dimensional visualization；
S7, three-dimensional quantitative analysis：
S7.1, the volume that root system in soil is obtained by the volume fraction volume fraction of Avizo；And/or
S7.2, obtain regarding each independent root system as an object by auto skeleton modules, analyze each object and join
Number, and total parameter of root system in whole sample is analyzed, the parameter for analyzing each object includes the position of each object of analysis, angle
Degree, ligancy, surface area, node（node）Number, Node distribution, equivalent redius, length, line segment number, end node points, branch's section
Points and isolated node, in step S7.2, the total parameter for analyzing root system in whole sample includes analyzing root system in whole sample
Cumulative volume, total length, total nodes, total end node points, total score nodes, total isolated node, root quantity are average long
Degree, average equivalent radius, total length.
The present invention gathers first and in-situ root system is gathered in sample ground soil, and sampling function substantially reduces disturbing in sampling process
Dynamic, the method combined with Avizo softwares using CT scan 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 combine soft
The skeletonization method of part realizes the three-dimensional quantitative analysis of root system of plant space structure, and these quantized datas include plant roots coefficient
Amount, equivalent diameter, ligancy, pore throat quantity etc..
Presently preferred embodiments of the present invention is the foregoing is only, not to limit the present invention, all essences in the present invention
Within god and principle, any modification, equivalent substitution and improvements made etc. should be included within the scope of the present invention.
Claims (6)
1. it is a kind of based on CT scan technology quantify root system spacial framework method, it is characterised in that：Comprise the steps：
S1, sample collection：Pvc pipe is pressed into into soil, whole pvc pipe is sealed and blocked with PVC lids after taking out, do not disturbed
Dynamic soil root；
S2, CT scan：Sample is lain against CT scan equipment to be scanned；
S3, data strengthen：Image obtained by CT scan is imported to and is rebuild in Avizo softwares, and Fourier is passed through to image
Leaf wave filter and Gaussian filter eliminate image noise, strengthen picture quality；
S4, threshold method, further include：
S4.1, combined with Global thresholding using growth method, chosen using the conjury stick in the Segmentation plates of Avizo
The threshold value of root system, then adjusts threshold range around this threshold value, until comprising the root system for needing research in the image for showing；
S4.2, select 3D options, it will whole root system is shown in display window, by expansion and erosion in menu bar, no
Disconnected adjustment and the perfect root systems for obtaining more；
S5, image cutting and binaryzation：By Avizo cutting tools, chosen area, the crack that portion disturbances are produced, profit are rejected
With the threshold method of step S4, the binary map of root system in soil is obtained；
S6, three-dimensional visualization：Rendered by the volume of Avizo and surface rendering, realize the three-dimensional visualization of soil root；
S7, three-dimensional quantitative analysis, further include：
S7.1, the volume that root system in soil is obtained by the volume fraction of Avizo；And/or
S7.2, obtain regarding each independent root system as an object by Auto skeleton modules, analyze each object and join
Number, and analyze total parameter of root system in whole sample.
2. the method for quantifying root system spacial framework based on CT scan technology according to claim 1, its feature exists
In：The pipe range of the pvc pipe is 50cm, internal diameter 10cm.
3. the method for quantifying root system spacial framework based on CT scan technology according to claim 1, its feature exists
In：In step S2, the parameter of CT scan equipment is voltage 140KV, electric current 200mA, sweep span 0.625mm.
4. the method for quantifying root system spacial framework based on CT scan technology according to claim 1, its feature exists
In：In step S6, realize making video while three-dimensional visualization.
5. the method for quantifying root system spacial framework based on CT scan technology according to claim 1, its feature exists
In：In step S7.2, the parameter for analyzing each object includes the position of each object of analysis, angle, ligancy, surface area, section
Points, Node distribution, equivalent redius, length, line segment number, end node points, branch node number and isolated node.
6. it is according to claim 5 based on CT scan technology quantify root system spacial framework method, it is characterised in that：
In step S7.2, the total parameter for analyzing root system in whole sample includes analyzing the cumulative volume of root system in whole sample, total length, always
Nodes, total end node points, total score nodes, total isolated node, root quantity, average length, average equivalent radius, always
Length.
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| 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 |
| CN109829941A (en) * | 2019-01-04 | 2019-05-31 | 华南农业大学 | A kind of root system of plant 3-d modelling measurement method based on central line pick-up |
| CN113390905A (en) * | 2021-05-31 | 2021-09-14 | 北京师范大学 | Method for quantifying pore space structure of soil aggregate based on CT scanning technology |
| CN116309560A (en) * | 2023-05-17 | 2023-06-23 | 北京师范大学 | Method and system for detecting moisture distribution of plant catheter |
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Cited By (8)
| 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 |
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| CN113390905A (en) * | 2021-05-31 | 2021-09-14 | 北京师范大学 | Method for quantifying pore space structure of soil aggregate based on CT scanning technology |
| 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 |
| CN116309560A (en) * | 2023-05-17 | 2023-06-23 | 北京师范大学 | Method and system for detecting moisture distribution of plant catheter |
| 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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