3D visualization and finite element mesh formation from wood anatomy samples, Part I - Theoretical approach

The work summarizes created algorithms for formation of finite element (FE) mesh which is derived from bitmap pattern. Process of registration, segmentation and meshing is described in detail. C++ library of STL from Insight Toolkit (ITK) Project together with Visualization Toolkit (VTK) were used for base processing of images. Several methods for appropriate mesh output are discussed. Multiplatform application WOOD3D for the task under GNU GPL license was assembled. Several methods of segmentation and mainly different ways of contouring were included. Tetrahedral and rectilinear types of mesh were programmed. Improving of mesh quality in some simple ways is mentioned. Testing and verification of final program on wood anatomy samples of spruce and walnut was realized. Methods of microscopic anatomy samples preparation are depicted. Final utilization of formed mesh in the simple structural analysis was performed.
The article discusses main problems in image analysis due to incompatible colour spaces, samples preparation, thresholding and final conversion into finite element mesh. Assembling of mentioned tasks together and evaluation of the application are main original results of the presented work. In presented program two thresholding filters were used. By utilization of ITK two following filters were included. Otsu filter based and binary filter based were used. The most problematic task occurred in a production of wood anatomy samples in the unique light conditions with minimal or zero colour space shift and the following appropriate definition of thresholds (corresponding thresholding parameters and connected methods (prefiltering + registration) which influence the continuity and mainly separation of wood anatomy structure. Solution in samples staining is suggested with the following quick image analysis realization. Next original result of the work is complex fully automated application which offers three types of finite element mesh. Tetrahedral mesh is coded for FE analysis with significant gradients and hexahedral mesh is offered for tasks with low gradients. Modified octree code is introduced for future research of anisotropic combined mesh.

Keywords: ITK, FEM, image converter to FE mesh, hexahedral and tetrahedral mesh, octree, wood anatomy

Grants and funding:

The Research project GP106/06/P363 Homogenization of material properties of wood for tasks from mechanics and thermodynamics (Czech Science Foundation) and Institutional research plan MSM6215648902 - Forest and Wood: the support of functionally integrated forest management and use of wood as a renewable raw material (2005-2010, Ministry of Education, Youth and Sport, Czech Republic) supported this work. This work benefited from the use of the Insight Segmentation and Registration Toolkit (ITK), open source software developed as an initiative of the U.S. National Library of Medicine.