About Axonarium

Axonarium is an open, evidence-graded knowledge base of neural connectivity. Every connection is an aggregate of cited claims, each tagged with species, method and confidence. It starts with the rodent amygdala and its human homologues, and grows one circuit at a time toward whole-brain and brain–body coverage.

What is in it today

The mouse amygdala's connections at the level of brain regions, from the Allen Mouse Brain Connectivity Atlas (Oh et al. 2014): every target of anterograde tracer injected into an amygdala nucleus of a wild-type mouse, and every amygdala nucleus that injections elsewhere label. Each experiment and target is one claim, with its projection density. See them on the 3D brain and network, in the connection table, or region by region. Regions come from the Allen mouse and human atlases via BrainGlobe, mapped to UBERON (Atlases).

Reading the evidence

A connection is never typed by hand: it is computed from its claims, and opens them. A claim is accepted when at least half of the injected tracer was in the region it names, and proposed when most of it spread elsewhere; regions that received tracer themselves are never counted as targets. Densities pool both hemispheres. Claims from the Allen atlas are made when the site is built and shown here with their citation, but are not redistributed in the downloadable data, following the Allen Institute's terms.

What comes next

Rat connectivity, human homology, cell-type-specific connections, and claims from the published literature, drafted by AI agents and checked by independent verifier agents and human audit. Progress is tracked in the status page and the sprint cards on GitHub.

How it is built

The knowledge lives as plain YAML files in a public GitHub repository. Humans and AI agents change it only through pull requests, which must pass automated checks: the schema, every identifier and citation looked up in its registry, retracted papers flagged, and deletions reviewed by a person. This site and its database are rebuilt from those files on every merge.

Licences

Project-curated data is licensed under CC BY 4.0, and code under Apache-2.0. Data from other sources keeps its own terms, recorded per source.

Citing

Cite the repository (see CITATION.cff) and the original papers behind the claims you use; every claim links to its source.

Contributing

Read CONTRIBUTING.md and the open sprint cards on GitHub.