Launching Navigate

First Launch (Recommended)

After installation, validate your setup by launching in synthetic hardware mode first:

navigate -sh

Once the software opens in synthetic mode, configure your hardware next. We recommend using the configurator:

navigate -c

Follow the quick setup checklist in Configuring Navigate.

After hardware configuration is complete, launch navigate normally:

navigate

Note

Use synthetic hardware mode whenever the computer is not connected to microscope hardware.

Launch by Installation Strategy

Conda + PyPI

If you followed Conda + PyPI:

conda activate navigate
navigate -sh
navigate

venv + PyPI

If you followed venv + PyPI:

# Windows (cmd/powershell)
.venv\Scripts\activate

# Linux/Mac
source .venv/bin/activate

navigate -sh
navigate

Install from GitHub

If you followed Install from GitHub, activate the environment where you installed navigate, then launch:

navigate -sh
navigate

uv Installation

If you followed uv Installation:

# Activate the uv-created environment
# Windows (cmd/powershell)
.venv\Scripts\activate

# Linux/Mac
source .venv/bin/activate

navigate -sh
navigate

Command Line Arguments

Run navigate --help to see all available options.

Core arguments

Core command line arguments
Argument	Description
-h, --help	Show available command line arguments.
-sh, --synthetic-hardware	Launch without attached hardware (recommended for first launch, testing, and setup).
-c, --configurator	Open the configuration wizard for creating/editing hardware configuration files.

Additional useful arguments

These arguments are not typically used, but can be helpful for advanced users. For example, by pointing navigate to different configuration files, you can easily switch between microscopes without modifying the default files. More detail about these files, and their role in navigate, can be found in Software Configuration. For a full list of arguments, run navigate --help.

Additional command line arguments
Argument	Description
-d	Enable the debugging tool menu.
--config-file PATH	Use a non-default `configuration.yml`.
--gui-config-file PATH	Use a non-default `gui_config.yml`.
--experiment-file PATH	Use a non-default `experiment.yml`.
--waveform-constants-file PATH	Use a non-default `waveform_constants.yml`.
--waveform-templates-file PATH	Use a non-default `waveform_templates.yml`.
--rest-api-file PATH	Use a non-default `rest_api_config.yml`.
--logging-config PATH	Use a non-default `logging.yml`.
--multi-positions-file PATH	Use a non-default `multi_positions.yml`.

Tip

If you are running Windows with Conda, you can create a desktop shortcut to navigate by right-clicking the Desktop, selecting New, then Shortcut, and entering %windir%\system32\cmd.exe "/c" C:\path\to\miniconda\Scripts\activate.bat navigate && navigate in the location field.