> For the complete documentation index, see [llms.txt](https://docs.neurolabai.io/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.neurolabai.io/start-using-neurolab/brain-explorer.md).

# Brain Explorer

Neurolab's Brain Explorer provides a rich interface for moving from the numbers in a report into visualized brain regions, networks, tracts, circuits, and supporting context. The Brain Explorer keeps different brain-related channels separate so that a useful visualization is not mistaken for a measurement or causal claim.

## Start from the report

Open Brain Explorer from a completed report whenever possible. The report supplies the compound, route, model release, facts-and-evidence release, and available localization channels. Report-linked navigation helps keep the selected brain context tied to the result that produced it.

Reference reports can also be used to learn the interface and compare visualization modes. They are examples, not substitutes for a query-specific result.

## Channel meanings

| Channel                         | What it can represent                                      | What it does not establish                              |
| ------------------------------- | ---------------------------------------------------------- | ------------------------------------------------------- |
| Raw GNN parcel ranking          | Relative known-route model output over 392 parcels         | Measured activation, dose response, or a causal pathway |
| Receptor-density hypothesis     | Localization suggested by receptor-density references      | Functional engagement or occupancy                      |
| Circuit-localization hypothesis | Symbolic localization through typed circuit relationships  | A dynamical simulation or propagation trace             |
| Literature evidence             | Source-scoped brain records when independently available   | A complete literature review or model validation        |
| Measured map                    | A measurement only when the report explicitly supplies one | Transfer to another compound, dose, or population       |
| Legacy compatibility            | Earlier behavior retained for diagnosis or comparison      | Current validation                                      |

## Guided exploration

The guided tour introduces fourteen topics across orientation, channel choice, regional interpretation, network context, tract and circuit views, evidence, provenance, and limitations. Use it to learn what each control changes before drawing a conclusion from color or geometry.

Regional exploration can provide readable anatomy briefs and retrieve relevant report or reference context. These briefs can be cached for navigation, but cached explanatory text is not a new model output and should not override the report's evidence state.

## Regions, networks, tracts, and circuits

* **Regions and parcels** locate ranked or referenced anatomy.
* **Networks** group regions under a declared atlas or reference framework.
* **Tracts** provide anatomical connection context when present.
* **Circuits** organize typed mechanism hypotheses across receptors, regions, tracts, and functions.

None of these layers should be interpreted as proof that a compound activates, traverses, or causally controls the displayed system. The active channel and its method label determine what the visualization means.

## Human-readable parcel labels

The report can add `name`, `section`, and `hemi` metadata to entries in `brain_top20_parcels_specific`. The resolver covers all 392 outputs: 360 Glasser cortical parcels and 32 Tian S2 subcortical parcels.

Readable labels improve navigation and exports without changing the original parcel identifier or numerical model output.

## A safe reading sequence

1. Confirm the report, route, and active channel.
2. Read the channel's method and validation label.
3. Treat values as relative within that channel unless its contract says otherwise.
4. Use labels and briefs to locate anatomy, not to infer mechanism.
5. Inspect evidence, provenance, and reliability separately.
6. Preserve parcel identifiers and release metadata in exports.

Next: [How to Read a Neurolab Report](/start-using-neurolab/report-interpretation.md)


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# Agent Instructions
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## Querying This Documentation
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