navigate

open source light-sheet microscope control

navigate is an open-source Python package for light-sheet microscope control. It supports reconfigurable hardware setups and automated acquisition routines.

OS compatibility: navigate is primarily used on Windows for microscope operation because many hardware drivers are Windows-focused. Linux and macOS are useful for development and limited testing.

Documentation

Project documentation is published at: https://thedeanlab.github.io/navigate/

Key entry points:

• Getting Started: https://thedeanlab.github.io/navigate/01_getting_started/03_software_installation.html
• Configure navigate: https://thedeanlab.github.io/navigate/01_getting_started/05_configuring_navigate.html
• Developer Install: https://thedeanlab.github.io/navigate/03_contributing/02_developer_install/02_developer_install.html
• Contributing Guidelines: https://thedeanlab.github.io/navigate/03_contributing/01_contributing_guidelines/01_contributing_guidelines.html

Quick Install (Conda + PyPI)

Install Miniconda: https://docs.conda.io/en/latest/miniconda.html

conda create -n navigate python=3.9.7
conda activate navigate
pip install navigate-micro

First Launch (Recommended)

# 1) Validate in synthetic hardware mode
navigate -sh

# 2) Open the configurator to create/edit configuration files
navigate -c

# 3) Launch normally
navigate

Install From Source (Developers)

git clone https://github.com/TheDeanLab/navigate.git
cd navigate

Install in editable mode with development dependencies:

# Windows (cmd/powershell)
pip install -e .[dev]

# Linux/macOS
pip install -e ".[dev]"

Command Line Arguments

Run navigate --help for the complete list.

• -h, --help: show help text.
• -c, --configurator: open the configuration wizard.
• -sh, --synthetic-hardware: launch without attached hardware.
• -d: enable the debugging tool menu.
• --config-file PATH: use a non-default configuration.yaml.
• --gui-config-file PATH: use a non-default gui_configuration.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.

Contributing

If you plan to contribute, follow the contributor docs linked above. Before opening a PR, run:

pre-commit run --all-files
pytest
conda run -n navigate make -C docs html -j 15

Need help or want to report a bug? Open an issue: https://github.com/TheDeanLab/navigate/issues