Release Notes for Iso2mesh Version 1.0.1

code name: Mapo Tofu - update 1, released on Jun. 03, 2011

1. Introduction
2. About this release
3. What's new compared to 1.0.0
4. System requirement
5. Known issues
6. Acknowledgement

1. Introduction

Iso2mesh is a free, powerful, yet easy-to-use 3D mesh generator for Matlab and Octave. It is particularly suitable for creating high-quality surface and tetrahedral meshes from 3D medical imaging data, including binary, segmented or gray-scale volumetric images. Iso2mesh is cross-platform, quantitative, versatile, and fully optimized for better speed and low-memory requirement.

Iso2mesh toolbox contains over 90 modular Matlab functions, covering 3D volumetric image pre-processing (hole-filling, thinning and thickening), surface mesh modeling (extraction, remeshing, repairing, and smoothing), volumetric mesh creation, plotting and import/export for a range of mesh file formats. For some of the core functions, iso2mesh calls the self-contained meshing utilities built upon CGAL and tetgen to perform Delaunay tetrahedralization, a process known for producing high-quality, self-intersection-free surfaces and volumetric meshes.

2. About this release

Iso2mesh v1.0.1 is the first update to the stable release v1.0.0 announced 3 months ago. This release focuses on fixing bugs and issues reported by the users to enhance the stability and overall consistency. The meshing out from v1.0.1 is mostly identical to v1.0.0, except for 64bit Linux distributions where we added new binaries to utilize large memory (>4GB).

3. What's new compared to 1.0.0

The iso2mesh 1.0.1 update gained the following compared to 1.0.0:

  1. it allows users to generate large meshes (>4GB memory) on 64bit Linux systems
  2. you can plot color-coded surface plots using plotmesh (the 4th column of node input represents the nodal values)
  3. v2m and vol2mesh now accept a new option "cgalpoly"
  4. plotmesh/volface now output all surface triangles in counter-clockwise orientation
  5. savemedit output supports the label column
  6. added edgeneighbors to report neighboring triangles in a surface

Particularly, the new 'cgalpoly' option gives user an open-source pipeline to generate tetrahedral meshes and completely by-passes the non-free tetgen step.

The detailed change logs can be found in the ChangeLog and SVN commit history pages.

4. System requirement

To install the iso2mesh version 1.0.x, you need

  1. at least 17MB free disk space for the all-in-one package, and 4~8MB for platform-specific packages
  2. a computer running Windows 95, XP, Vista and 7 (32/64bit), or GNU Linux (32/64bit) or Mac OSX (Intel)
  3. a working directory where you have write-permission
  4. Matlab 7.0+ or GNU Octave 3.0+
  5. for efficient mesh processing, 1GB or more memory is recommended

To use fillhole3d or run some of the demo scripts, you need to install the image processing toolbox for Matlab or image toolbox for Octave.

5. Known issues

  1. when using the cgalpoly option with surf2mesh, the input surface nodes are not preserved in the output mesh
  2. to set opt.autoregion=1 can make the meshing 3x to 5x slower due to use of finddisconnsurf
  3. automatically detect face vs elem in plotmesh is not 100% robust
  4. iso2mesh can not automatically process surfaces that intersect each other. One can use remeshsurf to repair a single self-intersecting mesh, but more than 2 such surfaces can be a trouble
  5. if your mesh contains multiple disjointed components, iso2mesh (cgalsurf) may sometimes miss a few, you can try different RNG seeds

6. Acknowledgement

We deeply appreciate the contribution from the CGAL team, who has done a marvelous work to develop state-of-the-art image-based mesh generation utilities. We also want to thank Hang Si for his great work for writing tetgen, which is heavily involved in iso2mesh's meshing work-flow.

For those of you who has used iso2mesh in your work, the author of this toolbox appreciates if you can cite the following paper in your publication, this will help tremendously for the future development of this software:

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

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