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 rotuines.

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

• optional arguments:

  • -h, --help show this help message and exit

• Input Arguments:

  • -sh, --synthetic_hardware
  • --config_file CONFIG_FILE
  • --experiment_file EXPERIMENT_FILE
  • --etl_const_file ETL_CONST_FILE
  • --rest_api_file REST_API_FILE
  • --logging_config LOGGING_CONFIG

Authors

• Kevin Dean
• Zach Marin
• Xiaoding 'Annie' Wang
• Dax Collison
• Sampath Rapuri
• Samir Mamtani
• Renil Gupta
• Andrew Jamieson