navigate is an open source Python package for control of light-sheet microscopes. It allows for easily reconfigurable hardware setups and automated acquisition rotuines.
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]'
.
Please refer to and contribute to the documentation, which can be found on GitHub Pages: https://thedeanlab.github.io/navigate/.
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.