Implement the control libraries

Begin by installing the packages in a virtual environment. For more information on why virtual environments matter, refer to this page.

git clone https://github.com/Alienor134/UC2_Fluorescence_microscope.git
cd UC2_Fluorescence_microscope
git submodule update --init --recursive
conda create -n control python=3.10
conda activate control
cd ControlSerial
pip install -e .
cd ..
cd ControlMotors
pip install -e .
cd ..
cd ControlCamera
pip install -e .
cd ..
cd ControlLight
pip install -e .

Install the libraries required for Arduino following the README instructions in ControlSerial and ControlMotors.

[optional]

If you want to install a data management strategy, implement the data management directly at the instrument level using Sacred. Then use the Altar suite to interact with the data.

Example of project

You can find an example of a project using the fluorescence microscope here. It corresponds to the code used for the project manuscript - TODO.

• The folder CSL-experiments explains how to connect the fluorescence microscope to the database framework Sacred and store the data in MongoDB. It contains several examples of codes used to generate the raw data for the manuscript - TODO.

• The folder CSL-analysis access the database using the Python package Incense and show how to analyse the data. It corresponds to the data presented in manuscript - TODO.