physion 0.1.1

Vision Physiology Software

Vision Physiology Software

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

Simply:

pip install physion

For an installation on an acquisition setup

conda env create -n acquisition -f acquisition_environment.yml

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.