Research On Automatic Measuring Method Of 3d Root System Architecture In Situ

Root system is the important organ of plant for absorbing water and nutrients from soil.Root research is one of the important research topics in physiology and morphology.Root system architecture(RSA)is the spatial formation and distribution of root system in the soil.,Including root spatial adjacent relationship and hierarchical relationship.RSA directly affects the ability of plants to absorb and transport water and nutrients.Therefore,the study of RSA is a key issue in plant research.However,due to the particularity of the root growth environment and the complexity of the architecture,traditional root measurement tools and methods cannot complete root measurement in situ,quickly,non-destructively and accurately.In order to solve the above problem,Agricultural Imaging Detection Technology Laboratory(AIDTL)in SCAU has conducted a series of studies on plant root imaging in situ based on X-ray CT,Root CT Images denoising and segmentation,the technoiogies of 3D visualization and measuring basic parameters of RSA based on visual model.The emphases of research in this thesis is to further explore the rapid extraction method of plant root 3D vector model.Then based on this model,complete root measurement in situ,quickly,nondestructively and accurately.Finally build a prototype system to integrate related algorithms.The content of this article is as follows:(1)Root CT images acquiring and processing in situ.The 160 kv industrial CT designed by AIDTL was used to collect plant root samples planted in culture soil.During the studies,a total of 3 sets of representative root sample CT images were collected.Sample 1 is a 1486-layer 16-bit tomographic image with 512 × 512 resolution,Sample 2 is a 338-layer 16-bit tomographic image with 484 × 484 resolution,Sample 3 is a 339-layer 16-bit tomographic image with 484 × 484 resolution.Plant root samples is filtered and segmented.And then,those samples is used as the initial data source.(2)The building of 3D vector model of plant root in situ.Firstly,according to the linear characteristics of the root system,the slice algorithm was used to extract skelecon points of plant root.Then establishing the root branch topology by path planning algorithm based on connectivity.Finally reconstruct each root branch and slice the root branch to get the root node attributes(radius,area,perimeter.etc.)to form the root vector model.Data structures(root slices,root nodes,root branches,etc.)are designed to store the vector model data.(3)Automatic measurement of RSA parameters.The root vector model is used as a data model to complete automatic measurement of RSA parameters.According to the root morphological characteristics,a total of 22 RSA parameters were counted in this paper.Those parameters can be divided into two classes: root system and root branch.Root system parameters include: root length,volume,surface area,and so on.Root branch parameters include: branch level,branch length,branch volume and so on.(4)The implementation of RSA parameters measurement system.In the Qt interface application development framework,using C + + programming language and open source computer vision library OpenCV,medical image segmentation and registration toolkit ITK(Insight Segmentation and Registration Toolkit)and 3D visualization toolkit VTK(Visualization Toolkit)to achieve this article The relevant algorithm proposed.And design a prototype system to integrate related algorithms.(5)Algorithm verification and data analysis.A total of three root samples were collected as test samples.In oreder to verify the accuracy and effectiveness of the measurement nethod,the manual measurement results were compared with the system measurement results.At the same time,quantitatively analyze the execution time to test algorithm execution efficiency.In summary,the emphase of research in this thesis were concerned on the building method of 3D vector model of plant root and the automatic measurement methods of RSA parameters in situ.Then developed the RSA parameters measurement system.The system realizes the functions of 3D visualization,3D vector model construction,measurement and anaiysis of RSA parameters.An effective technology platform is provided to the root researchers.