GAMer - Geometry-preserving Adaptive Mesher

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 other applications. GAMer has the following main features:

  • Surface mesh improvement and decimation algorithms

  • Boundary marking and other features

  • Estimation of surface curvatures

  • Generation of mesh surfaces around biological molecules

Technical Features:

  • Code is implemented in C++ and supports Python using a pybind11 wrapper (pygamer).

  • Cross system compilation using CMake and runs on Linux (64 bit), Windows (32 or 64 bit) or MacOS (64 bit).

  • Blender addon which enables easy access to GAMer features using the PyGAMer API.

  • Uses the Colored Abstract Simplicial Complex data (CASC) structure as the flexible underlying representation of surface and tetrahedral meshes.

  • Code is hosted at GitHub under the Lesser GNU public license (LGPLv2). Please post issues or reports there.

Acknowledging the Use of GAMer in Your Work

The contributors to this project are grateful for your use of this software. To acknowledge our contributions please cite the following:

Referencing the Code: GAMer Zenodo

Reference manuscript:

@article{,
  title = {An Open Source Mesh Generation Platform for Biophysical Modeling
           Using Realistic Cellular Geometries},
  author = {Lee, Christopher T. and Laughlin, Justin G. and Moody, John B.
            and Amaro, Rommie E. and McCammon, J. Andrew
            and Holst, Michael J. and Rangamani, Padmini},
  year = {2020},
  month = jan,
  issn = {0006-3495},
  doi = {10.1016/j.bpj.2019.11.3400},
  journal = {Biophysical Journal},
}

Technical manuscript:

@article {Lee_gamer2_534479,
  author = {Lee, Christopher T. and Laughlin, Justin G.
            and Angliviel de La Beaumelle, Nils and Amaro, Rommie
            and McCammon, J. Andrew and Ramamoorthi, Ravi
            and Holst, Michael J. and Rangamani, Padmini},
  title = {GAMer 2: A System for 3D Mesh Processing of
           Cellular Electron Micrographs},
  elocation-id = {534479},
  year = {2019},
  doi = {10.1101/534479},
  publisher = {Cold Spring Harbor Laboratory},
  URL = {https://www.biorxiv.org/content/early/2019/01/29/534479},
  eprint = {https://www.biorxiv.org/content/early/2019/01/29/534479.full.pdf},
  journal = {bioRxiv}
}

Legacy Contributions

  • GAMer 1 was originally developed by Zeyun Yu, Yuhui Cheng, and Michael Holst. To acknowledge your use of GAMer 1 please cite:

    @article{Yu_gamer_2008,
  author = {Yu, Zeyun and Holst, Michael J.
            and Cheng, Yuhui and McCammon, J. Andrew},
  title = {{Feature-Preserving Adaptive Mesh Generation for
            Molecular Shape Modeling and Simulation}},
  journal = {J. Mol. Graph. Model.},
  issn = {10933263},
  year = {2008},
  month = jun,
  volume = {26},
  number = {8},
  pages = {1370--1380},
  doi = {10.1016/j.jmgm.2008.01.007},
  url = {https://dx.doi.org/10.1016/j.jmgm.2008.01.007},
}

  • The BlendGAMer addon is inspired by work from Tom Bartol (Salk Institute) and Johan Hake who developed the original addon for GAMer 1.

Getting Started:

Tutorials and Examples:

API Documentation:

For Developers:

Indices and tables