License and Citation

License & Citation

License

golgi is free and open-source software under the GNU Affero General Public License, version 3 or later (AGPL-3.0-or-later) — see LICENSE.

This is required by the dependency stack, not an arbitrary choice:

• TetGen (the volume mesher core compiled into the tetgen wheel) is AGPL-3.0 (dual-licensed; a commercial license is available from WIAS). Linking it makes the combined work AGPL — this is the decisive reason golgi is AGPL.
• Gmsh (import gmsh) is GPLv2-or-later, upgradeable to AGPLv3 — compatible.
• golgi serves a Trame browser GUI, so the AGPL §13 "Remote Network Interaction" clause applies to networked use.

Full inventory and verified per-package licenses are in THIRD_PARTY_LICENSES.md.

Compatibility flags (confirm with counsel before redistribution)

1. PyFibers is GPL-2.0-only (no "or later"), which is not one-way compatible with AGPLv3. golgi mitigates this by running the PyFibers→NEURON fiber step and the TetGen mesher in separate subprocesses that exchange data through files (an argument for mere aggregation, not one linked work). PyFibers also carries a non-commercial field restriction.
2. AxonML is proprietary (Duke OTC T-008477; non-commercial/academic only) — not open source and not AGPL-compatible. golgi never bundles or redistributes it; it is an optional plug-in loaded only if the user has separately obtained it and accepted Duke's terms. The default NEURON/PyFibers path needs no such backend.

Commercial / closed-source redistribution

golgi imposes no restriction beyond the AGPL terms. But because both meshers are copyleft, shipping golgi inside a closed-source or commercial product additionally requires separate commercial licenses for TetGen (WIAS) and Gmsh, plus resolution of the PyFibers/AxonML field-of-use terms above.

Data

Data released alongside golgi — the micro-CT imaging datasets and the golgi study bundles on Zenodo — is licensed separately under CC-BY-4.0.

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Citation

If you use golgi in your research, please cite:

• the methods paper — PLOS Computational Biology (in review);
• the companion software paper — SoftwareX (in review);
• the archived software release on Zenodo — 10.5281/zenodo.21281594 (concept DOI, always resolving to the latest release; v1.0.0 is 10.5281/zenodo.21301866).

The reproduction data and replay-verified study bundles are archived separately at 10.5281/zenodo.21300944 — cite that when you reuse the figure data. A study bundle records the exact software version it was built with, so citing one pins the version unambiguously.

Please also acknowledge the upstream tools golgi builds on — FEniCSx/DOLFINx, PETSc, TetGen, Gmsh, NEURON/PyFibers, PyVista, Trame — and the IT'IS tissue database.

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See also

Reproducible Study Bundles · Reproducing the Paper · Contributing