Configuration Reference

Configuration Reference

A reference for the parameters and environment variables that control golgi. GUI controls, the Study setters, and the project's ui_state.json all write the same state keys.

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Mesh parameters

Set via Study.set_mesh(**kwargs) or the Mesh drawer. See Meshing.

Key	Meaning
use_epi	generate/include an epineurium shell
epi_thickness_um	epineurium shell thickness (µm)
lc_endo_um	endoneurium element size (µm)
lc_epi_um	epineurium element size (µm)
lc_muscle_um	muscle / far-field element size (µm)
lc_scar_um	encapsulation/scar element size (µm)
lc_saline_um	cuff saline element size (µm)
lc_silicone_um	cuff silicone element size (µm)
lc_contact_um	electrode contact element size (µm)
decim_target_k	imported-surface decimation target (thousands of triangles)
muscle_radial_pad_mm, muscle_axial_pad_mm	far-field bath padding (mm)
muscle_dx_mm, muscle_dy_mm, muscle_dz_mm	far-field bath offsets (mm)

Conductivities

Anisotropic, frequency-aware tissue properties — full table and the Cole–Cole / IT'IS / perineurium model are on Conductivity & Tissue Properties. Keys include sigma_endo, sigma_endo_long, sigma_epi, sigma_muscle, sigma_muscle_long, sigma_saline, sigma_silicone, sigma_contact, sigma_scar, and the perineurium options perineurium_ci, sigma_peri, peri_thk_m, perineurium_species.

Electrode / cuff

Set via Study.set_electrodes([...]) or the Designs drawer; full parameter lists per electrode type are on Electrodes & Cuff Designer. Common keys: electrode_type, name, eid, cuff_anchor (trunk/branched/centroid), cuff_offset_mm, L_cuff_mm, cuff_clearance_mm, cuff_wall_mm, contact_polarities, contact_current_fractions.

Fiber seeding

Set via Study.set_fiber_seed(**kwargs) or the Import wizard's Fibers step. See Fiber Populations & Trajectories.

Key	Meaning
n_fibers	number of seed points
fiber_method	streamlines (curved) or axial (straight)
fiber_max_steps	max streamline integration steps
fiber_seed_end	which cap to seed from
fiber_cluster_eps_mm	cap-clustering radius (branch separation)
fiber_cap_band_pct	z-band near each extremum searched for caps
fiber_min_rel_size_pct	minimum relative cap-cluster size to keep
fiber_axial_normal_thresh	"axialness" threshold for cap facets
fiber_auto_detect_branches	auto-find branches vs fixed count

FEM / simulation

Set in the Simulate ▸ Extracellular field (FEM) panel. See Finite-Element Solver.

Control	Meaning
stimulus current	total injected current (mA)
solver preset	Quick / Balanced / HPC (Krylov tolerance + AMG tuning)
configs to solve	which polarity configs to solve
compute access impedance	run the DC dual-solves for Z_access

Sweeps

SweepRequest (golgi/jobs/schemas.py) — mode (recruitment/threshold), amplitudes_mA, bisect_lo_mA/bisect_hi_mA/bisect_tol_uA, fiber_indices, branch_filter, fiber_type_filter, pulse_params, backend (pyfibers/axonml), model_name. See Recruitment Sweeps & Selectivity.

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Environment variables

Variable	Purpose
GOLGI_EMIT_IMPEDANCE	enable DC access-impedance dual-solves (default on)
GOLGI_EMIT_RECORDING	emit per-contact reciprocity lead fields for CNAP (default off)
GOLGI_RECIP_CI	use the two-field perineurium contact-impedance solver
GOLGI_GROUND_OUTER_FALLBACK	ground the full exterior when no muscle bbox is present
GOLGI_FEM_RUNNER	slurm to dispatch FEM to a cluster (else local)
GOLGI_SLURM_PARTITION / _CPUS / _MEM_GB / _TIME / GOLGI_SBATCH	SLURM runner config / sbatch path (or the fake-sbatch shim)
GOLGI_MPIRUN	MPI launcher (mpirun / mpiexec / srun)
GOLGI_FI_PROVIDER / FI_PROVIDER	libfabric provider — pin to tcp on single-rank macOS
SDKROOT	macOS SDK path for the FFCx JIT (auto-detected if unset)
GOLGI_TEST_NERVE / GOLGI_DEMO_STL	override the test/example nerve geometry

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See also

Meshing · Conductivity & Tissue Properties · Electrodes & Cuff Designer · Finite-Element Solver · Troubleshooting & FAQ