Iso2mesh: an image-based 3D surface and volumetric mesh generator


  • Author: Qianqian Fang <q.fang at neu.edu>
    • Department of Bioengineering
    • Northeastern University
    • 360 Huntington Ave, Boston, MA 02115
  • Version: 1.7.9 (Deviled Egg - beta)
  • License: GPL v2 or later (see COPYING)
    • (this license does not cover the binaries under the bin/
    • directory, see Section III for more details)
  • URL: http://iso2mesh.sf.net

Table of Content

1. Introduction
2. Overview of the functions
3. Acknowledgement

1. Introduction

"Iso2mesh" is a MATLAB/Octave-based mesh generation toolbox, designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, working either independently or interacting with external free meshing utilities. Iso2mesh toolbox can directly convert a 3D image stack, including binary, segmented or gray-scale images such as MRI or CT scans, into quality volumetric meshes. This makes it particularly suitable for multi-modality medical imaging data analysis and multi-physics modeling. Above all, iso2mesh is open-source. You can download it for free. You are also allowed to extend the toolbox for your own research and share with other users. Iso2mesh is cross-platform and is compatible with both MATLAB and GNU Octave (a free MATLAB clone).

The details of this toolbox can be found in the following paper:

  • Qianqian Fang and David Boas, "Tetrahedral mesh generation from volumetric binary and gray-scale images," Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2009), pp. 1142-1145, 2009

2. Overview of the functions

Creation of high-quality surface and tetrahedral meshes from volumetric images has been a challenging task. There are very limited software and resources available for this purpose. Commercial tools, such as Mimics and Amira, are both expensive and limited in functionalities. Iso2mesh was developed as a free alternative to these expensive commercial tools and provides researchers a highly flexible, modular and streamlined image-based mesh generation pipeline. Intuitive interfaces and rich functionalities allow one to enjoy a wide range of mesh-based analyses, ranging from 3D volumetric image pre-processing (hole-filling, thinning and thickening), surface mesh modeling (extraction, remeshing, repairing, and smoothing) to volumetric mesh creation.

Converting 3D image stacks into quality surface and tetrahedral meshes is one of the core features of iso2mesh. We provide serveral automated functions to perform the image->mesh and mesh->image conversion, including

  • vol2mesh (v2m): convert a 3D volumetric image into a tetrahedral mesh
  • vol2surf (v2s): extract triangular surfaces from a 3D image volume
  • surf2mesh (s2m): create a tetrahedral mesh from a triangular surface mesh
  • surf2vol (s2v): rasterize a close-surface into a volumetric image

Most of these function are associated with several meshing options and parameters to give users full control to mesh density, adaptivity, region labeling and mesh quality. The output data for some of these functions can be used as the input for the others, giving endless combinations to analyze your data. In addition to image-based mesh generation, iso2mesh can also mesh geometry primitives such as spheres, cubes and cylinders. This makes iso2mesh a CAD-capable software, fully integrated in the MATLAB/Octave environments.

Another core feature of iso2mesh is surface mesh processing. A surface mesh is the bridge between a voxelated image and a tetrahedral mesh, and is the foundation for successful 3D mesh generation. In iso2mesh, we provide the following key functions for surface mesh processing:

  • smoothsurf (sms): smoothing a surface mesh
  • surfboolean: boolean operations (join, intersect, diff) of two surfaces
  • meshresample: downsample a surface mesh to a coarse surface
  • meshrefine: refine a surface mesh
  • remeshsurf: remesh a surface mesh, including up-sampling and down-sampling
  • meshcheckrepair: test a surface mesh and remove defects and self-intersecting elements

A third area iso2mesh excels is the rich set of mesh analysis and inquiry functions. For both surface and tetrahedral meshes, iso2mesh can report the element volume (or area), mesh quality metrics, node connectivity and neighbors, interior edges and boundaries, surface norms, element centroids, etc.

Last, but not the least, iso2mesh can import and export mesh data from/to a dozen of file formats, including those used by the popular FEA software like COMSOL and ABAQUS. The STL format can export an iso2mesh-generated mesh for 3D printing. Users can not only export the data to a file, but also make 3D plots in MATLAB/Octave using the powerful "plotmesh" function.

These examples are only a small fraction in the over 100 optimized functions provided by iso2mesh. The modular design of iso2mesh makes the code easy to understand and easy to be intergrated in your data analysis workflow. Please check out the full iso2mesh function list and detailed help information in the following URL:

http://iso2mesh.sf.net/cgi-bin/index.cgi?Doc/FunctionList

3. Acknowledgement

This toolbox interacts with a number external meshing tools to perform the essential functionalities. These tools are listed below:

bin/tetgen

  • Summary:tetgen is a compact and fast 3D mesh generator
  • License: GNU Affero General Public License version 3
  • URL: http://tetgen.org/
  • Author: Hang Si <si at wias-berlin.de>
Research Group: Numerical Mathematics and Scientific Computing
Weierstrass Institute for Applied Analysis and Stochastics
Mohrenstr. 39, 10117 Berlin, Germany

bin/cgalsurf

bin/cgalmesh and bin/cgalpoly

  • Summary: cgalmesh and cgalpoly are utilities to produce surface and volumetric meshes from a multi-valued volumetric image
  • Source: it is a slightly modified version from Mesh_3 example from CGAL 3.5
  • License: CGAL v3 core library is licensed under QPL (Q Public License) other modules are under the Lesser General Public License (LGPL)
  • URL: http://www.cgal.org/Manual/3.5/doc_html/cgal_manual/Mesh_3/Chapter_main.html

bin/cgalsimp2

bin/jmeshlib

  • Summary: meshfix is adapted from the sample code of JMeshLib
  • License: GPL (GNU General Public License) v2 or later
  • URL:http://jmeshlib.sourceforge.net/
  • Author:Marco Attene <attene at ge.imati.cnr.it>
Istituto di Matematica Applicata e Tecnologie Informatiche
Consiglio Nazionale delle Ricerche
Via De Marini, 6 (Torre di Francia)
16149 Genoa - ITALY

bin/meshfix

  • Summary: meshfix is a mesh-repairing utility
  • License: GPL (GNU General Public License) v2 or later
  • URL:http://code.google.com/p/meshfix/
  • Author: Marco Attene, Mirko Windhoff and Axel Thielscher.
Istituto di Matematica Applicata e Tecnologie Informatiche
Consiglio Nazionale delle Ricerche
Via De Marini, 6 (Torre di Francia)
16149 Genoa - ITALY

bin/gtsset and bin/gtsrefine

  • Summary: GTS is the GNU Triangulated Surface Library
  • License: LGPL (GNU Lesser General Public License)
  • URL:http://gts.sourceforge.net/
  • Author: GTS developers

Note: iso2mesh and the above meshing utilities are considered as an "aggregate" rather than "derived work", based on the definitions in GPL FAQ (http://www.gnu.org/licenses/gpl-faq.html#MereAggregation) Therefore, the license of iso2mesh and these utilities are independent. The iso2mesh license only applies to the scripts and documentation/data in this package and exclude those programs stored in the bin/ directory. The source codes of the modified meshing utilities are available separately at iso2mesh's website and retain their upstream licenses.

Your acknowledgement of iso2mesh in your publications or presentations would be greatly appreciated by the author of this toolbox. The citation information can be found in the Introduction section.

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