Code for experimental setups and analysis pipelines to study cellular and network physiology in visual cortical circuits

The software is organized into several modules to perform the acquisition, the preprocessing, the visualization and the analysis of multimodal recordings (see Documentation below).

1. Install a python distribution for scientific analysis:

   get the latest Miniconda distribution and install it on your home folder.

2. Run the following in the Anaconda prompt:

   clone the repository using git:

   git clone https://github.com/yzerlaut/physion --recurse-submodules
   

   to create the physion environment and perform the installation, run:

   cd physion
   conda env create -f environment.yml
   

   For an installation on an acquisition setup, see the dedicated instructions

After the installation, the program is the launched from the Anaconda prompt by typing:

conda activate physion	
python -m physion

The different modules of the software are documented in the following links:

• Visual stimulation -- relying on PsychoPy
• Performing multimodal recordings
• Intrinsic Imaging
• Electrophysiology
• Calcium imaging -- pipeline based on Suite2P
• Pupil tracking
• Behavioral monitoring
• Assembling pipeline
• Hardware control
• Visualization -- relying on the excellent PyQtGraph
• Analysis

Use the dedicated Issues interface of Github.