GAMer is a surface mesh improvement library developed to condition surface meshes derived from noisy biological imaging data. Using Tetgen, GAMer can generate tetrahedral meshes suitable for finite elements simulations of reaction-diffusion systems among others. GAMer has the following main features:
Technical Features:
Thanks for using GAMer! The developers would love to hear how you are using the tool. Please send us an email or post on GitHub letting us know.
Please cite the above Zenodo DOI to acknowledge the software version and cite the following papers:
Lee, C. T.; Laughlin, J. G.; Moody, J. B.; Amaro, R. E.; McCammon, J. A.; Holst, M.; Rangamani, P. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophysical Journal 2020, 118 (5), 1003–1008.
The following instructions are to build the base GAMer library. If you wish to additionally compile the Blender GAMer addon, GAMer documentation, or other features please refer to the Additional Options section prior to building.
First, download a copy of the source from releases or clone the master branch.
git clone https://github.com/ctlee/gamer.git
cd gamer
Linux and Mac:
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr -DGAMER_TESTS=on -DCMAKE_BUILD_TYPE=Release ..
make
For Windows, we support building using Microsoft Visual Studio (MSVS) through the use of CMake generators:
mkdir build64
cd build64
cmake -DBUILD_BLENDGAMER=TRUE -G "Visual Studio 15 2017 Win64" -A x64 ..
cmake --build . --config Release
For a complete guide to installation, including configuration of PyGAMer and BlendGAMer please checkout the online installation documentation.
GAMer uses Tetgen to generate tetrahedralizations.
GAMer uses Eigen to compute eigenvalues/eigenvectors of the Local Structure Tensor.
GAMer uses casc as the underlying simplicial complex data structure.
GAMer uses GoogleTest to handle testing.
GAMer uses Pybind11
Mesh checks in the GAMer Blender addon are inspired or borrowed from 3D Print Toolbox by Campbell Barton and Meshalyzer from CellBlender.
Triangle is also bundled with GAMer but not currently used.