Mathematical Biophysics
Understanding living systems
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Table of Contents
Segmentation and Meshing tools for Image-based Modelling
Credits: Russell Garwood, Yongle Sun (Manchester), Jon Hill (York), Susheel Varma (Sheffield)
Overview
| Visualisation & segmentation | Platform | Cost | Comment |
|---|---|---|---|
| FUJI / ImageJ + 3D Viewer | all | 0 | Highly flexible image processing, with limited 3D rendering and meshing |
| 3D Slicer | all | 0 | VTK-based 3D visualisation and segmentation of medical images |
| ParaView | all | 0 | VTK-based 3D simulation data visualisation, a free analogue to TecPlot, Origin, Igor Pro, etc. |
| Blender | all | 0 | Free alternative to 3D Studio / Autodesk Maja with some mesh manipulation |
| Drishti | Win/Mac | 0 | Advanced visualisation and rendering for presentations & outreach; basic meshing |
| SPIERS | Win/Mac | 0 | Tomographic visualisation, serial rendering and meshing |
| Seg3D + ImageVis3D | all | 0 | Visualisation and segmentation of medical images |
| FEI Avizo / Amira | all | $$ | Powerful 3D visualisation, image processing and segmentation |
| OsiriX | Mac only | $ | DICOM data visualisation, FDA-certified for diagnostics |
| Meshing Software | Platform | Cost | Comment |
|---|---|---|---|
| Gmsh, TetGen, Netgen | all | 0 | Flexible command line tools (gmsh is also with a user-unfriendly GUI) |
| MeshLab | all | 0 | Triangular & tetrahedral GUI mesh manipulator; can be unstable for big meshes |
| enGrid + Netgen | all | 0 | Tetrahedral + prismatic meshing GUI optimised for CFD; integrated with OpenFOAM |
| iso2mesh | all | 0 | Flexible tetrahedral meshing Toolbox for MATLAB / Octave with COMSOL support |
| CGAL | all | 0 | Very flexible C++ meshing and computational geometry library |
| libMesh | all | 0 | C++ meshing library |
| vmtk | all | 0 | Vascular Modeling Toolkit: Python/C++ library for centreline tracing and surface meshing |
| CRIMSON | Win/Linux | 0 | Vasculature-oriented segmentation & meshing GUI tool for image-based modelling |
| COMSOL Multiphysics | all | $ | Built-in physics-based meshing and mesh-optimisation (STL import tips) |
| ANSYS Meshing | Win/Linux | $$$? | CFD-oriented robust meshing (formerly ANSYS ICEM CFD; see also OptiGrid) |
| Autodesk Netfab | Win only | $$$? | Geometry and mesh manipulation |
| FEI Avizo / Amira + XWind | all | $$ | Powerful segmentation with limited tetrahedral meshing |
| Materialise Mimics | Win only | $$$? | Complete workflow with robust meshing but restrictive GUI; optimised for 3D printing |
| Simpleware ScanIP + FE | Win only | $$$ | Complete workflow with robust meshing for FE solvers, CFD-optimised with COMSOL support |
Summary: MeshLab, Gmsh, Simpleware are good GUI tools for simple-to-medium mesh-generation; for high-throughput tasks, use script-based Gmsh, Netgen, TetGen, CGAL, iso2mesh (all are highly flexible), and also ANSYS ICEM.
Tip: test the final mesh quality by plotting the distribution of dihedral angles.
Amira / Avizo Tips
Credits: Kathy Tinoco, Cornelia Vacar (FEI), Philip Pearce (MIT), Alexander Erlich and Sebastian Gilbert (Manchester)
Manual Skeletonisation as an alternative to Auto Skeleton module:
- Compute a distance map from your label field, using Distance Map module. Set the Chamfer Weights to float
- Convert the result to 8-bit data via Convert Image Type module
- Generate a centerline tree (spatial graph) with Centerline Tree module (this step may take a while)
- Centerline Tree module has
Tube Parameters(slopeandzeroVal) that help to reduce the number of false side branches. E.g., for a thin noisy object, largezeroValuewill account for the noise when tracing a branch, and for a thick object with irregular surface, largeslopewill allow for larger local thickness variations.
— Igor Chernyavsky, 2017/08/17 17:47 —
