Mesh utility collections for neuron morphology reconstruction

A Quick Lookup Table: What tool should I use to open .xxx file?

Format	Content	View/Edit Tool
.swc	Point tracing morphology data	neuTube
.nrn	Instructions for NEURON morphology construction	NEURON
.stl	Triangular surface mesh	Meshlab
.off	Polygonal surface mesh	Meshlab
.obj	Polygonal surface mesh	Meshlab
.ply	Polygonal surface mesh	Meshlab
.blend	Surface model constructed using Blender	Blender
.geo	Gmsh geometry file	Gmsh
.msh	Tetrahedral volume mesh	Gmsh
.mesh	Finite element mesh	Gmsh
.poly	TetGen geometry	TetGen
.smesh	TetGen geometry	TetGen

Mesh utilities From OIST

A collection of meshing utilities for neuron morphologies, developed by the Computational Neuroscience Unit at Okinawa Institute of Science and Technology Graduate University, Japan.

For SWC morphology

• SWCIntersectDetect: Branch intersection detection for SWC/NEURON morphology.
  • Main Input: .swc morphology file
  • Main Output: .swc morphology file where branch intersections are labeled using user-defined tags
• SWCTetMesher: Tetrehedral mesh generator from SWC morphology data.
  • Main Input: .swc morphology file
  • Main Output: .mesh tetrahedral mesh file of the morphology. (Optional: .off surface mesh of the morphology)

For surface mesh morphology

• MultiCompMesher: Multi-component mesh generation and labeling from watertight surface boundaries.
  • Main Input:
    1. .off watertight surface boundary meshes.
    2. user-defined text file with component signatures.
  • Main Output: .mesh Tetrahedral mesh file of the morphology with labeled components.

For STEPS mesh annotation

• polyhedronROI: Create Region of Interest (ROIs) annotations in STEPS using watertight surface boundaries and labeling signatures.
  • Main Input:
    1. .off/.stl/.obj watertight surface boundary meshes.
    2. stepe.geom.Tetmesh object from STEPS.
  • Main Output: The same stepe.geom.Tetmesh object with ROI added.

Mesh utilities from other parties

For SWC morphology

• AnaMorph: Framework for creating 3d neuronal morphologies from point/diameter descriptions.
  • Main Input: .swc morphology file
  • Main Output: .obj watertight, manifold surface mesh of the morphology
• CTNG: A tool for constructing a 3d tesselation of a neuron's surface from point-diameter data.
  • Main Input: .swc morphology file
  • Main Output: text-based file with watertight, manifold surface mesh of the morphology

For surface mesh morphology

• GAMer: surface mesh improvement library developed to condition surface meshes derived from noisy biological imaging data. Also provides tetrahedral mesh generation functionality using TetGen backend.
  • Main Input: surface mesh files
  • Main Output: repaired and optimized surface meshes
• Gmsh: Tetrahedral mesh generator from CAD geometry or surface boundaries.
  • Main Input: surface morphology file
  • Main Output: .msh tetrahedral mesh file, can also export to other formats
• TetGen: Tetrahedral mesh generator from polyhedral surface boundaries.
  • Main Input: surface morphology file
  • Main Output: text-based tetrahedral mesh file
• TetWild: Robust tetrahedral meshing from polyhedral surface boundaries.
  • Main Input: surface mesh file
  • Main Output: gmsh tetrahedral mesh.
• VolRoverN: Pipeline solution for neuron reconstruction from RECONSTRUCT series files to surface/volume mesh. Also provides automatic surface mesh repairing and optimization functionality.
  • Main Input: RECONSTRUCT series files, or .off surface mesh
  • Main Output: surface/volume meshes of the reconstruction