physion -- Vision Physiology

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

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

Software screenshot

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Install

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

Getting started

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

conda activate physion	
python -m physion

Modules and documentation

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

Troubleshooting / Issues

Use the dedicated Issues interface of Github.