Configuring Navigate

This page is the fastest path to a first working microscope configuration in navigate.

The configuration.yaml file defines the hardware and microscope settings loaded at startup. By default, the local file is saved at:

  • Windows: C:\Users\Username\AppData\Local\.navigate\config\configuration.yaml

  • macOS/Linux: ~/.navigate/config/configuration.yaml

Warning

The configuration file is sensitive. A reliable strategy is to build a working setup using only virtual devices first, then replace devices with real hardware one at a time.

Tip

If you cannot locate configuration.yaml, launch with synthetic hardware (navigate -sh), then select File ‣ Open Configuration Files.

Configuration Wizard

  1. Activate the environment used for installation.

  2. Launch the configurator:

navigate -c

  1. Choose New Configuration to create a new file, or Load Configuration to edit an existing file.

  2. If needed, click Add A Microscope to create additional microscope entries.

  3. In each hardware tab, the first column shows configuration entries (most are likely required), the middle column is where you enter values, and the right column contains field help text.

  4. Fill required hardware fields (DAQ, camera, stage, lasers, filter wheel, etc.), validating one device at a time.

  5. Save as configuration.yaml in your local .navigate/config directory, then launch:

navigate
Navigate configuration wizard window.

Need More Control?

Manual editing supports advanced use cases such as:

  • multiple microscopes and inheritance,

  • stage axis mapping and flip behavior,

  • stage limits and offsets,

  • zoom calibration and stage-compensation tables.

For full details, see Advanced Software Configuration.