Tetrahedral Mesh Generator from SWC Morphology Data

This program reads a SWC morphology file (.swc) and generates a tetrahedral mesh using spherical interpolation of the morphology. A watertight triangular surface mesh of the morphology can also be exported during the process.

This program doesn't detect branch intersection of the SWC morphology. For this procedure, please visit https://github.com/CNS-OIST/SWCIntersectDetect

This program can not generate tetrahedral meshes from triangular surface meshes commonly generated from Electron Microscopic (EM) imaging. For this purpose please visit https://github.com/CNS-OIST/MultiCompMesher.

Prerequisite

• git
• a C++ compiler
• CMake
• CGAL
• Boost

Compilation

git clone https://github.com/CNS-OIST/SWCTetMesher.git
cd SWCTetMesher
mkdir build
cd build
cmake ..
make

Usage

The commands below assume you are still in SWCTetMesher/build

• Basic usage

  ./SWCTetMesher SWC-FILE
  

  • SWC-FILE: A .swc morphology reconstruction file.

    If a SWC file named example.swc is given, the tetrahedral mesh will be written to example.mesh. The output file can be changed using the -o option.

• Advance options

  • --output OUTPUT-FILE, or -o OUTPUT-FILE: Change the output location of the tetrahedral mesh. If OUTPUT-FILE doesn't end with .mesh, this suffix will be appended.
  • --surfmesh: Also output the triangular surface mesh. If enabled, the surface mesh will be written to OUTPUT-FILE.off
  • interp-distance: Maximum distance between two spheres in the interpolation. A shorter distance results in a more accurate interpolation, but longer meshing time.

Other parameters can be set to control the meshing process and optimize the mesh quality. You can list them using

./SWCTetMesher -h

The usage of these parameters can be found in the CGAL 3D mesh generation manual.

Concurrency (Parallel) mode

If Intel's TBB library is installed and found, the program will try to use concurrency mode for meshing. Users can disable it and use sequential mode instead by setting the ACTIVATE_CONCURRENCY flag during compilation

cmake -DACTIVATE_CONCURRENCY=OFF ..

Example

This example generates a tetrahedral mesh from a full Purkinje cell morphology. The SWC morphology is curated in advance using the data in Zang, etc., 2018.

We can visualize the morphology in neuTube

The command to generate the mesh is

# assumed still in SWCTetMesher/build

./SWCTetMesher example/purkinje.swc

The mesh is written to purkinje.mesh, then visualized in Gmsh. Note that each component is labeled and colored individually. To use the mesh in STEPS, the user needs to export it to the Abaqus inp format or the Gmsh 2.0 ASCii format in Gmsh.

The user can also export the surface mesh for postprocessing or visualization in applications such as Meshlab.

./SWCTetMesher example/purkinje.swc --surfmesh

Different parameters can be adjusted to generate a mesh with higher resolution, mainly fc-size, fc-distance and cc-size.

./SWCTetMesher ../example/purkinje.swc  --fc-distance 0.075 --cc-size 0.5