Getting Started

Getting Started

This page runs your first end-to-end study two ways — by script and in the GUI — and points you to the deeper pages for each stage. If you haven't installed golgi yet, do Installation first.

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Option A — your first study in Python (5 minutes)

The fastest way to see the whole pipeline is the bundled example, which runs on a built-in synthetic nerve (no data needed):

python examples/recruitment_sweep.py

It loads a nerve, meshes it, places a bipolar cuff, solves the anisotropic field, generates fiber trajectories, sweeps stimulus amplitude, writes a recruitment-curve PNG, and exports a reproducible study bundle. To run on your own surface:

python examples/recruitment_sweep.py --nerve /path/to/nerve.stl --project ./my_study

What the script does, step by step

import golgi
from golgi.jobs.schemas import SweepRequest

s = golgi.Study.create("vagus_study")          # a project dir on disk

s.import_nerve("nerve.stl")                     # 1. load a surface (STL/NAS/OBJ, mm)
s.set_mesh(use_epi=True, perineurium_ci=True)   # 2a. mesh + material options
s.set_electrodes([{                             # 2b. design a cuff
    "name": "Bipolar @ centre",
    "electrode_type": "bipolar ring-pair",
    "cuff_anchor": "centroid",
}])
s.run_mesh()                                    # 3. multi-region TetGen mesh
s.run_fem()                                     # 4. anisotropic FEM (lead fields)
s.set_fiber_seed(n_fibers=100,
                 fiber_method="streamlines")    # 5a. fiber-generation params
s.run_fibers()                                  # 5b. curved 3-D trajectories
result = s.run_sweep(SweepRequest(              # 6. recruitment across amplitude
    mode="recruitment",
    amplitudes_mA=[0.1, 0.25, 0.5, 1.0, 2.0]))
s.export_bundle("vagus_study.golgi")            # 7. hashed, replayable bundle
s.close()

Each numbered step maps to a pipeline stage and a wiki page:

Step	Method	Learn more
1	import_nerve	Geometry Import & Segmentation
2a	set_mesh	Meshing · Conductivity & Tissue Properties
2b	set_electrodes	Electrodes & Cuff Designer
4	run_fem	Finite-Element Solver
5	run_fibers	Fiber Populations & Trajectories
6	run_sweep	Recruitment Sweeps & Selectivity · Fiber Models & Activation
7	export_bundle	Reproducible Study Bundles

Full method reference: Python API.

Verify and share

golgi replay vagus_study.golgi      # byte-for-byte reproducibility check

Hand that one file to a colleague; golgi import + golgi replay reconstitutes and verifies the whole study. See Command-Line Interface.

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Option B — your first study in the GUI

golgi          # open the printed local URL in a browser

Then work top to bottom through the navbar:

1. Sign in / Create project on the welcome screen.
2. File ▸ Import Nerve — a 4-step wizard: Load nerve → Endoneurium → Fibers → Muscle. (Or File ▸ Segment µCT slice… to segment an image first.)
3. Designs — add a cuff, pick an electrode type, set per-contact polarities (or open the Cuff Designer for ASCENT-style presets).
4. Mesh — set per-region element sizes and Build mesh (TetGen).
5. Materials — set tissue conductivities (with the Cole–Cole evaluator) and Update.
6. Simulate ▸ Extracellular field (FEM) — pick a solver preset and Run FEM solve.
7. Simulate ▸ Single fiber / Fiber population / Sweep — compute thresholds and recruitment.
8. Export ▸ Export figures / Export report, and File ▸ Export study to share.

The complete tour, with every panel and control, is in the GUI Walkthrough.

Because the GUI and API share the same on-disk Study state, you can build a project in the browser and continue it from a script — or vice-versa.

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Where to go next

• Understand the model → Pipeline Overview
• Design electrodes → Electrodes & Cuff Designer
• Scale up → Headless / HPC
• Reproduce the paper → Reproducing the Paper
• Hit a snag → Troubleshooting & FAQ