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golgi is an open, graphical platform for image-to-recruitment modeling of peripheral nerve stimulation. It takes a peripheral nerve from image to stimulated fiber population through a single point-and-click interface — no programming required — and mirrors every step in a scriptable Python API and command-line interface. It builds anatomically realistic, multifascicular 3-D nerve models and computes fiber-type-selective recruitment end to end on a fully open finite-element stack with no commercial dependencies (no COMSOL, ANSYS or Abaqus).

This wiki is the full documentation. New here? Start with Installation → Getting Started → the illustrated Tutorial (a complete study, step by step with screenshots).

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The pipeline at a glance

flowchart LR
    A["Image / surface / mask"] --> B["Promptable segmentation"]
    B --> C["Multi-region tetrahedral mesh"]
    C --> D["Anisotropic FEM + perineurium CI"]
    D --> E["Fiber populations + curved 3-D trajectories"]
    E --> F["Activation thresholds (NEURON / AxonML)"]
    F --> G["Recruitment, selectivity, current steering"]
    G --> H["Hashed, replayable study bundle"]

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Each box is a documented stage — see Pipeline Overview.

What makes golgi different

• No-code GUI for the whole pipeline (Trame, browser-based) — see GUI Walkthrough.
• Fully open solver stack — FEniCSx/DOLFINx + TetGen/Gmsh, no COMSOL — see Finite-Element Solver.
• Genuine 3-D, branching anatomy with curved, fascicle-following fibers through bifurcations — see Fiber Populations & Trajectories.
• Realistic biophysics — NEURON/PyFibers and AxonML backends, Cole–Cole / IT'IS tissue properties, explicit perineurium contact impedance — see Fiber Models & Activation and Conductivity & Tissue Properties.
• Current steering & selectivity — arbitrary N-polar montages, recruitment curves, fascicular / branch selectivity, design comparison — see Recruitment Sweeps & Selectivity.
• Reproducibility built in — integrity-hashed, replayable study bundles.

Three interfaces, one study

Every operation acts on a single shared golgi.Study state, so a graphical session, a script, and a batch job are interchangeable.

Interface	Use it for	Page
Graphical UI	exploration, design, teaching — the primary interface	GUI Walkthrough
Python API (golgi.Study)	notebooks, batch studies, CI	Python API
Command line (golgi …)	clusters, automation, bundle verification	Command-Line Interface

Find your way

• I want to run my first model → Getting Started
• I want a guided, illustrated first run → Tutorial
• I want the GUI panel-by-panel reference → GUI Walkthrough
• I want to script it → Python API · Headless / HPC
• I want the science → Pipeline Overview · Finite-Element Solver · Fiber Models & Activation
• I want to design an electrode → Electrodes & Cuff Designer
• I want to reproduce / share results → Reproducible Study Bundles · Reproducing the Paper
• Something broke → Troubleshooting & FAQ
• What's a term mean? → Glossary

Project facts

• License: AGPL-3.0-or-later (data: CC-BY-4.0) — see License & Citation.
• Platforms: Linux, macOS.
• Status: companion to the methods paper (PLOS Computational Biology, in review) and software paper (SoftwareX, in review).