Release Notes for Iso2mesh v1.7.9

code name: Deviled Egg beta, released on September 19, 2015

: 1. Introduction
: 2. About this release
: 3. What's new compared to 1.5.0
: 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 GNU/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 130 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 v1.7.9 is a stable release towards the next generation iso2mesh, i.e. the "2.0" milestone. Compared to the previous stable release (v1.5), numerous new features and bug fixes were included. The number of functions in this toolbox grew by 10%; The support for Mac OS Yosemite is also included in this release.

3. What's new compared to 1.5.0

Compared to the version 1.5 released in July 2013, the 1.7.9 release gained the following features:

JSONlab update to 1.1
qmeshcut allows to exact plane that are exactly parallel to the faces
surf2mesh supports region-based volume control
meshrefine can insert external nodes to the mesh
allow binsurface to mesh a 2d image
significantly improved meshrefine - sizing field, new nodes etc
support OSX Yosemite
plotmesh supports plotting 3d polyline and loop objects
extract junction lines from a surface group
extractloops now supports open contours
latticegrid - 3D lattice function
GPU accelerated mesh rasterization - mesh2mask/mesh2vol/m2v (experimental)
add regular grid generation by meshgrid5 and meshgrid6
export to GMSH format (by Riccardo Scorretti)

With this new release, you will also benefit from many minor updates and bug fixes, including

fix getvarfrom workspace bug
fix s2m face label bug
fix plotmesh selector bugs
make v2m(method=cgalmesh) output repeatable

and many more.

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

4. System requirement

To install the iso2mesh version 1.7.9, you need

at least 32MB free disk space for the all-in-one package, and 6~12MB for platform-specific packages
a computer running Windows 95, XP, Vista and 7 (32/64bit), or GNU Linux (32/64bit) or Mac OS (Intel 32/64bit)
a working directory where you have write-permission to save intermediate outputs
Matlab 7.0+ or GNU Octave 3.0+
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 octave-image toolbox for Octave.

5. Known issues

surfboolean is experimental and may cause fail to run. This may be caused by a bug in the GTS library
when using the cgalpoly option with surf2mesh, the input surface nodes are not preserved in the output mesh
automatically detecting face vs elem in plotmesh is not 100% robust
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
if your mesh contains multiple disjointed components, iso2mesh (cgalsurf) may sometimes miss a few, you may add the volumetric image by 1 and remesh the domain

6. Acknowledgement

We deeply appreciate the contribution from the CGAL team, which has done a marvelous work for developing 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. Thanks also goes to Marco Attene, Mirko Windhoff, and Axel Thielscher for developing the "meshfix" utility, and to Donghyeon Kim, Blake Johnson, Niclas Borli and Peter Varga for their help in improving the toolbox.

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