> For the complete documentation index, see [llms.txt](https://zapit.gitbook.io/user-guide/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://zapit.gitbook.io/user-guide/using-the-gui.md).

# Using the GUI

- [Introduction: Using the GUI](https://zapit.gitbook.io/user-guide/using-the-gui/introduction-using-the-gui.md)
- [Scanner Calibration](https://zapit.gitbook.io/user-guide/using-the-gui/scanner-calibration.md): Calibrating the scanners to the camera view
- [Sample Calibration](https://zapit.gitbook.io/user-guide/using-the-gui/sample-calibration.md): Registering the sample to stereotaxic coordinate space
- [StimConfig Editor](https://zapit.gitbook.io/user-guide/using-the-gui/stimconfig-editor.md): Constructing Stimulus Sets
- [Generating stimulus patterns at the CLI](https://zapit.gitbook.io/user-guide/using-the-gui/generating-stimulus-patterns-at-the-cli.md): How to generate complicated stimulus patterns at the command line
- [Advanced Usage](https://zapit.gitbook.io/user-guide/using-the-gui/advanced-usage.md)