Meshing

Meshing

golgi builds multi-region tetrahedral meshes of the whole modeling domain — endoneurium, epineurium, perineurium interface, electrode contacts, cuff silicone, saline, and a surrounding tissue (muscle) bath — on an open meshing stack: TetGen (primary volume mesher) and Gmsh (geometry/extrusion). No commercial mesher is required.

Source: golgi/pipeline/mesh.py (driver), golgi/pipeline/plc.py (PLC assembly), golgi/pipeline/mesh_quality.py (quality metrics), golgi/compute/tetgen_runner.py and golgi/compute/gmsh_mesher.py (backends).

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How a mesh is built

1. Assemble the PLC (piecewise-linear complex) — the watertight surface description of every region and the electrode contacts, with region markers (plc.py, assemble_multi_domain_plc / assemble_bare_nerve_in_bath).
2. Tetrahedralize with TetGen, honoring per-region target sizes and quality switches.
3. Tag cells by region (the tags consumed by the solver and the conductivity model) and tag facets for the electrode contacts.
4. Score quality (per-region histograms) and surface it in the Mesh drawer.

The mesh is shared across electrode designs on the same nerve (the nerve and muscle bath are canonical), while each design's cuff is placed in its own local frame — so switching designs only moves the cuff, not the nerve geometry.

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Characteristic lengths

Each region has its own target element size (characteristic length, lc_*), set in the Mesh drawer or via Study.set_mesh(...). Finer near the contacts and inside the nerve, coarser in the far-field bath:

Parameter	Region
lc_endo_um	endoneurium (fascicle interior)
lc_epi_um	epineurium
lc_muscle_um	muscle / far-field bath
lc_scar_um	encapsulation / scar shell
lc_saline_um	cuff saline
lc_silicone_um	cuff silicone
lc_contact_um	electrode contacts

Tissue-region sizes are shared across designs; cuff-region sizes are per design. Smaller values give more accurate fields at higher mesh cost — the contacts and endoneurium dominate accuracy, so refine those first.

There is also a muscle bounding-box placement (radial/axial padding and x/y/z offsets) controlling the extent of the far-field bath and the ground boundary, plus a surface decimation target (decim_target_k) applied to the imported nerve before meshing.

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Mesh quality

After a build, golgi computes per-element shape quality and shows per-region histograms plus a combined view in the Mesh drawer (mesh_quality.py, figures/mesh_stats.py). Use these to catch slivers or under-refinement before spending solve time. Quality figures are exportable like any other (Figures & Reports).

golgi assumes the imported nerve surface is watertight. In-app mesh repair / Boolean editing is intentionally out of scope — repair non-manifold surfaces in MeshLab or Blender first. A light repair pass (pymeshfix) and decimation are applied, but a badly broken surface should be fixed upstream.

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TetGen vs Gmsh

• TetGen does the multi-region volume tetrahedralization from the PLC, with nerve_studio-style switches (small epsilon, near-180° angle tolerances) tuned for the thin cuff/contact features. TetGen's core is AGPL-licensed — which is part of why golgi is AGPL (see License & Citation).
• Gmsh provides OpenCASCADE geometry and extrusion (e.g. building a prismatic nerve from an extruded cross-section) and is available as an alternative mesher path.

The fiber-trajectory generator builds its own nerve-only tet mesh (decoupled from cuff position) so cap detection is robust regardless of where the cuff sits — see Fiber Populations & Trajectories.

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References

• Si H (2015). TetGen, a Delaunay-based quality tetrahedral mesh generator. ACM Trans Math Softw 41:11. — the volume mesher.
• Geuzaine C, Remacle J-F (2009). Gmsh: a 3-D finite element mesh generator with built-in pre- and post-processing facilities. Int J Numer Methods Eng 79:1309. — geometry/extrusion mesher.
• Pelot NA, Thio BJ, Grill WM (2019). On the parameters used in finite element modeling of compound peripheral nerves. J Neural Eng 16:016007. — multi-region nerve FE-model conventions.

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See also

Geometry Import & Segmentation · Finite-Element Solver · Conductivity & Tissue Properties · Configuration Reference