Tutorial

GUI Tutorial

Neural modeling, reimagined. This tutorial walks through the golgi graphical user interface (GUI) end to end — from creating an account to running a full peripheral-nerve stimulation study: imaging a nerve cross-section, reconstructing it in 3-D, placing a cuff electrode, meshing, solving the extracellular field, and simulating single-fiber and whole-population activation.

It is the guided, illustrated first run. For a terse panel-by-panel reference of every screen, see the GUI Walkthrough; for the science behind each stage, follow the cross-links into the reference pages.

Screenshots were captured on Version Alpha 2.4.1. The GUI is browser-based and, in these examples, runs against a local server at localhost:8080. Menu labels, panel names, and default values may drift slightly between releases.

Conventions. Menus and buttons are written in bold (e.g. FILE → Import Nerve). Field names are written in italics. Numeric values shown are the defaults or example values from the screenshots and are meant as a starting point, not a prescription.

---

How this tutorial is organized

It reads front-to-back as one continuous study, split into four chapters so no single page runs too long:

1. Accounts & Dashboard — the landing page, registration, sign-in, the home dashboard, the user menu, and profile settings.
2. Projects & Workspace — the project details dialog (Overview / Status / Activity), exporting a study from the dashboard, and a tour of the workspace shell.
3. Build a Model — the hands-on walkthrough from a raw µCT stack to a meshed, material-assigned nerve with a cuff: create the project → segment & extrude → set up nerve, fibers and muscle → design the cuff → mesh → assign conductivities.
4. Simulate & Export — solving the extracellular field, single-fiber and population simulation, and exporting figures, a PDF report, and a reproducible study bundle.

A Glossary defines the domain terms used throughout.

---

Concepts and the big picture

golgi models how an implanted electrode activates the axons inside a peripheral nerve. A complete study moves through a fixed pipeline, and the workspace top-menu is laid out left-to-right in exactly that order:

FILE → DESIGNS → MESH → MATERIALS → SIMULATE → EXPORT

The logical stages are:

1. Geometry. Obtain a 3-D nerve. You can import a ready-made surface, or — as in this tutorial — segment a micro-CT (µCT) slice and extrude it into a watertight nerve made of an epineurium plus one or more fascicles.
2. Fibers. Populate the fascicles with axon trajectories (the paths that nerve fibers follow along the nerve).
3. Electrode. Place one or more cuff electrode designs around the nerve.
4. Mesh. Discretize the whole assembly (nerve, muscle, saline, silicone, contacts) into a tetrahedral finite-element mesh.
5. Materials. Assign an electrical conductivity to every tissue and material region.
6. Extracellular field (FEM). Solve the quasi-static electric field the electrode produces inside the nerve.
7. Fiber response. Feed that field into cable models of axons to predict which fibers fire — first for a single fiber, then for a realistic population.
8. Export. Bundle the figures, a PDF report, and a fully reproducible study archive.

Each stage caches its results, so you can revisit a project, reopen it, and pick up where you left off without recomputing everything. This same on-disk state also drives the Python API and command line — see the Pipeline Overview for the whole flow.

---

Next: Accounts & Dashboard →