Metadata-Version: 2.1
Name: physion
Version: 0.1.0
Summary: Vision Physiology Software
Author-email: Yann Zerlaut <yann.zerlaut@gmail.com>
Project-URL: Homepage, https://github.com/yzerlaut/physion
Project-URL: Bug Tracker, https://github.com/yzerlaut/physion/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

<!--<div><img src="https://github.com/yzerlaut/physion/raw/master/docs/physion.png" alt="physion logo" width="35%" align="right" style="margin-left: 10px"></div>-->

<div><img src="./docs/physion.png" alt="physion logo" width="35%" align="right" style="margin-left: 10px"></div>

# Vision Physiology Software

> *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](README.md#modules-and-documentation)).

### Software screenshot

<p align="center">
  <img src="doc/screenshot.jpg"/>
</p>

--------------------

## 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](src/physion/visual_stim/README.md) -- relying on [PsychoPy](https://psychopy.org)
- [Performing multimodal recordings](src/physion/exp/README.md)
- [Intrinsic Imaging](src/physion/intrinsic/README.md)
- [Electrophysiology](src/physion/electrophy/README.md)
- [Calcium imaging](src/physion/Ca_imaging/README.md) -- pipeline based on [Suite2P](https://github.com/MouseLand/suite2p)
- [Pupil tracking](src/physion/pupil/README.md)
- [Behavioral monitoring](src/physion/behavioral_monitoring/README.md) 
- [Assembling pipeline](src/physion/assembling/README.md)
- [Hardware control](src/physion/hardware_control/README.md)
- [Visualization](src/physion/dataviz/README.md) -- relying on the excellent [PyQtGraph](http://pyqtgraph.org/)
- [Analysis](src/physion/analysis/README.md)

## Troubleshooting / Issues

Use the dedicated [Issues](https://github.com/yzerlaut/physion/issues) interface of Github.
