navigate

open source light sheet microscope control

navigate is an open source Python package for control of light-sheet microscopes. It allows for easily reconfigurable hardware setups and automated acquisition routines.

Quick install

Download and install Miniconda.

conda create -n navigate python=3.9.7
conda activate navigate
pip install git+https://github.com/TheDeanLab/navigate.git

To test, run conda activate navigate and launch in synthetic hardware mode with navigate -sh. Developers will have to install additional dependencies with pip install -e '.[dev]'.

Documentation

Please refer to and contribute to the documentation, which can be found on GitHub Pages: https://thedeanlab.github.io/navigate/.

Command Line Arguments

Below are the optional arguments that can be passed to the navigate software:

• -h, --help Provides information on the optional arguments that can be passed to navigate.
• -sh, --synthetic_hardware Open the software without any hardware attached for testing and setting up a new system.
• -c, --configurator Open the navigate configuration wizard, which provides a graphical interface for setting up the hardware configuration.
• -d Enables the debugging menu in the software.
• --config-file Pass a non-default configuration.yaml file to navigate.
• --experiment_file Pass a non-default experiment.yaml file to navigate.
• --gui-config-file Pass a non-default gui_config.yaml file to navigate.
• --waveform-constants-file Pass a non-default waveform constants file to navigate.
• --rest_api_file Pass a non-default REST API file to navigate.
• --logging_config Pass a non-default logging configuration file to navigate.