# ToFScope user guide

ToFScope allows you to explore ToF-SIMS acquisitions using linked plots, named signals, and 3D views. It runs as a headless Python service in your terminal with an interface in your browser.

The guides for [installation](../../docs/getting-started/installation.md) and [your first analysis](../../docs/getting-started/first-analysis.md) cover the first steps. The installation guide also covers updates, uninstalling, and troubleshooting.


# Using ToFScope

- [Signals and views](../../docs/using-tofscope/signals-and-views.md): choosing ion channels, defining mass windows, and exploring regions and frame ranges.
- [Depth calibration](../../docs/using-tofscope/depth-calibration.md): connecting acquisition frames with known physical depths.
- [Peak identification](../../docs/using-tofscope/identification.md): searching isotope candidates and measuring selected signals.
- [3D visualization](../../docs/using-tofscope/3d-visualization.md): comparing spatial signals as overlays or tiles.
- [Saving and exports](../../docs/using-tofscope/saving-and-exports.md): preserving an analysis or sharing CSV and image results.
- [Preparing raw acquisitions](../../docs/using-tofscope/raw-preparation.md): creating initial ion maps when a file contains raw events.


# Technical documentation

The [architecture guide](../../docs/technical-documentation/architecture.md) explains the browser, service, calculations, and files through diagrams. [File compatibility and limitations](../../docs/technical-documentation/file-compatibility.md) describes supported files and how saved copies can be used in ToF-SIMS software. Developers and administrators can continue to [configuration](../../docs/technical-documentation/configuration.md), [building and testing](../../docs/technical-documentation/building-and-testing.md), and [deployment](../../docs/technical-documentation/deployment.md).

> **Note: Saving before stopping the service**
>
> Open analyses and in-progress jobs are held in memory. **Save as** creates a copy that can be reopened after a restart.