A Method Of Centerlines Extraction For 3D Model Of Plant Roots

Root is an important organ for plant,and different architectures of roots have an important influence in the absorption efficiency of water and nutrients.Plant roots in situ architecture refers to the spatial shape and distribution of the root system in soils and other medium,and generally includes two-dimensional(2D)and three-dimensional(3D)architecture.To obtain the 3D architecture parameters accurately of plant roots grown in soil medium,many scholars at home and abroad had applied X-ray computed tomography(XCT)technology to the in-situ architecture detection of roots.Firstly,XCT imaging equipment is used to acquire the images of in-situ root that growth in soil medium.Then,the root region is segmented from the images,and the 3D root models including the solid model and the surface model are obtained by the reconstruction algorithm.To obtain the 3D architecture or phenotypic parameters of the plant roots,the 3D model obtained needs to be vectorized to construct a 3D vector model of the plant root,to reduce the storage capacity of the root model,simplify parameter calculation,and improve the accuracy of calculation.Among them,the accurate extraction of the root centerline is the key step to the 3D model vectorization.The centerline of the 3D model,also known as the curve skeleton,provides a method that can effectively and compactly represent the target.It is an important research content in the fields of computer vision and computer graphics.It can be used to describe,match,and identify objects.It has an extensive value in use.At the same time,the extraction of the centerline and skeleton,especially the extraction of the 3D centerline,is also a challenging field of research.Although people have proposed many methods for different research objects and different research purposes,so far there is still lack of general-purpose algorithms,and the performance of the centrality,continuity,and other characteristics that extracted by different methods is variously.For the basic requirements of quantitative measurement of 3D root architecture for centrality,continuity and other characteristics,it is necessary to explore a centerline extraction method that suitable for the 3D root model,and then to accurately measure the 3D architecture parameters of the in-situ roots.This undoubtedly has important theoretical value and practical significance.The main work of this paper is as follows:(1)Analyze of centerline extraction algorithm.Through the literature reading,the research status of the centerline extraction method at home and abroad was understood.For three types of model,the centerline extraction methods for various types of models are applied for comparison analysis and testing.The experimental results show that the algorithm of mesh contraction has a better applicability on the root models.(2)Studying the centerline extraction algorithm based on mesh contraction of the 3D root models.1)Pre-processing of the 3D roots model.The 3D roots image is filtered and dilated to reduce the problem of fracture and noise of the model.After that,mesh simplification is performed for the reconstructed surface mesh model to reduce the redundant data.2)Centerline extraction by mesh contraction.Building tangent Laplacian operator for the mesh models,and the contraction is achieved by iteratively solving the contraction equation.After the iteration is ended,a mesh model with approximate 1D curves is obtained.Finally,the 1D root centerline is obtained by removing unnecessary mesh boundaries.3)Post-processing of the centerline.The centralization step is introduced to solve the centerline offset problem that caused by the shrinking process.The topological relationship is built,and the spline curve is fitted to the centered centerline to obtain a smooth centerline with a topological relationship.(3)Improved algorithm testing and analysis.The centerline extraction experiment was performed on different roots of the proposed algorithm,and the existing centerline extraction methods were compared and analyzed.Then,the angle and length parameters of the root branches were calculated and compared with the results of manual measurements.The results show that the method does not need complicated parameter adjustment process and has good applicability to different shape of root models.At the same time,the parameter measurement results confirm the feasibility of using the centerline obtained by the method for the measurement of root architecture parameters.(4)Developing a 3D centerline extraction system for plant roots.Using C++ programming language,combined with VTK and Qt and other libraries,adopting objectoriented thinking for system development.The implementation includes a series of functions such as the proposed centerline extraction algorithm,root model reconstruction and visualization.