# Documentation


- **Getting started**
- [Overview](/docs/overview): Data Hub automatically ingests, processes, and visualizes data generated by scientific instruments in the lab. Start here to install the watcher, manage access, and onboard instruments.
- [Quickstart](/docs/quickstart): Go from nothing to your first uploaded run in about ten minutes: install the watcher, point it at your instrument's output folder, and start watching.
- [Concepts](/docs/concepts): Short definitions of the core Data Hub vocabulary: watcher, instrument, run, run detection, stability period, upload modes, heartbeats, and events.

- **For lab operators**
- [Installing a watcher](/docs/installing-a-watcher): Set up the Data Hub watcher on a lab instrument PC to monitor a directory, upload new files, and report run data to the web app.
- [Adding an instrument](/docs/adding-an-instrument): Onboard a new lab instrument to Data Hub end to end: register it, activate it, and start uploading runs.
- [Run as a Windows service](/docs/windows-service): Install and operate the Data Hub watcher as a Windows service so it starts automatically on boot, survives logouts, and auto-updates in the background.
- [Upgrading the watcher](/docs/upgrading-the-watcher): Keep instrument PCs on the latest watcher release with background auto-update, on-demand self-update, version pinning, and rollback.
- [Troubleshooting](/docs/troubleshooting): Fix the watcher by symptom: won't start, files not detected, files not uploading, auto-update never fires, connection errors, and where to find the logs.

- **Administration**
- [Managing instruments](/docs/managing-instruments): The administrator side of instruments: confirming pending registrations, understanding instrument states, and deactivating instruments.
- [Managing watchers](/docs/managing-watchers): The watcher fleet from the admin side: monitoring health, deregistering watchers, approving manual uploads, and rolling releases across the fleet.
- [Managing tokens](/docs/managing-tokens): Create, use, and revoke personal access tokens that authenticate the watcher and other clients with the Data Hub REST API.
- [Security & permissions](/docs/security): Roles and what each can do, personal-access-token scopes, how authentication works, and good token hygiene.

- **Reference**
- [Architecture](/docs/architecture): How Data Hub fits together: the watcher, S3 storage, the Lambda processor, the API and web app, and the data flow from instrument to dashboard.
- [Watcher CLI](/docs/cli-reference): Every data-hub-watcher command, subcommand, and flag in one place: init, watch, upload, config, service, and self-update.
- [Watcher configuration](/docs/configuration-reference): Every config.yaml field, the ~/.data-hub file layout, environment variables, run-detection presets, upload modes, and the initial-scan behavior.
- [API reference](/docs/api-reference): The Data Hub REST API: authentication, scopes, every v1 endpoint grouped by resource, the MCP server, and the standard error shape.
- [MCP server](/docs/mcp-server): Query instruments, runs, files, and watcher data from AI clients like Claude Desktop and Cursor through the Data Hub Model Context Protocol server.
- [FAQ](/docs/faq): Short answers to common Data Hub questions: multiple watchers, revoked tokens, environments, run detection, manual uploads, and more.