| Author | Qianqian Fang |
| <q.fang at neu.edu> | |
| Department | Bioengineering |
| Institute | Northeastern University |
| Address | 360 Huntington Ave, Boston, MA 02115 |
| Version | 1.9.8 (Pot Stickers) |
| 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 |
"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 over 200 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 papers (citing the first paper is highly encouraged):
The first paper published recently describes a fully automated high-quality brain mesh generation pipeline built upon Iso2Mesh, providing a showcase for nearly all core functionalities provided in this toolbox.
In addition to convenient 3D mesh generation functionalities, the development of Iso2Mesh has also resulted in a number of submodules that have also received wide adoption - some are even more popular than Iso2Mesh itself. For example:
Currently, Iso2Mesh and its submodules are broadly distributed among popular open-source MATLAB toolboxes, especially among major neuroimaging tools, including
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 Simpleware, are both expensive and limited in flexibility. 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 meshvol2surf (v2s): extract triangular surfaces from a 3D image volumesurf2mesh (s2m): create a tetrahedral mesh from a triangular surface meshsurf2vol (s2v): rasterize a close-surface to a volumetric imagemesh2vol (m2v): rasterize a tetrahedral mesh to a volumetric imageMost 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 meshsurfboolean: boolean operations (join, intersect, diff) of two surfacesmeshresample: downsample a surface mesh to a coarse surfacemeshrefine: refine a surface meshremeshsurf: remesh a surface mesh, including up-sampling and down-samplingmeshcheckrepair: test a surface mesh and remove defects and self-intersecting elementsA 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 200 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
The default release of Iso2Mesh packages already contains pre-compiled binaries for a wide range of platforms (32/64bit Windows, 32/64bit Linux and Mac with 64bit Intel and 32 bit PowerPC CPUs). So, without needing to recompile, Iso2Mesh can be executed out-of-box on MATLAB or GNU Octave.
However, in the event that your operating system is not supported, or
due to license restrictions, such as creating a release for various
Linux distributions, you can recreate the mesh utility binaries under
iso2mesh/bin folder using the source codes provided under iso2mesh/tools
by following the below commands:
git clone --recurse-submodules https://github.com/fangq/iso2mesh.git
cd iso2mesh
rm -rf bin/*.mex* bin/*.exe
cd tools
make clean
makeThis will download and recompile the below binaries in the bin folder:
Once these binary files are recreated, you can run all the major functionalities of Iso2Mesh. The gtrefine utility is depreciated and replaced by cork and tetgen.
To compile the above external tools, the below tools must be pre-installed (tested on Ubuntu 14.04 LTS, if you use another Linux distribution, the package names might be different)
you can install these on Ubuntu by running:
sudo apt-get install gcc cmake libcgal-dev libsuitesparse-dev zlib1g-devon Ubuntu or Debian. If you use Fedora, you need to install the below packages
sudo dnf install cmake CGAL-devel SuperLU-devel blas-static gcc-c++ zlib-devel octave-develThis toolbox interacts with a number external meshing tools to perform the essential functionalities. These tools are listed below:
bin/tetgen and bin/tetgen1.5:
bin/cgalsurf:
bin/cgalmesh and bin/cgalpoly:
bin/cgalsimp2:
bin/jmeshlib:
bin/meshfix:
bin/cork:
bin/gtsrefine:
bin/PoissonRecon:
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.