phy is an open source neurophysiological data analysis package in Python. It provides features for sorting, analyzing, and visualizing extracellular recordings made with high-density multielectrode arrays containing hundreds to thousands of recording sites.
phy contains the following subpackages:
- phy.cluster: an API for manual sorting, used to create graphical interfaces for neurophysiological data
- phy.gui: a generic API for creating desktop applications with PyQt.
- phy.plot: a generic API for creating high-performance plots with VisPy (using the graphics processor via OpenGL)
phy targets developers and doesn't provide any I/O code. It only provides Python routines to process and visualize data.
The phy-contrib repo contains a set of plugins with integrated GUIs that work with dedicated automatic clustering software. Currently it provides:
- KwikGUI: a manual sorting GUI that works with data processed with klusta, an automatic clustering package.
- TemplateGUI: a manual sorting GUI that works with data processed with Spyking Circus and KiloSort (not released yet), which are template-matching-based spike sorting algorithms.
Note: the installation instructions will be simplified soon.
Make sure that you have miniconda installed. You can choose the Python 3.6 64-bit version for your operating system (Linux, Windows, or OS X).
Download the environment file.
Open a terminal (on Windows,
cmd, not Powershell) in the directory where you saved the file and type:
conda env create -n phy source activate phy # omit the `source` on Windows pip install phy phycontrib
Done! Now, to use phy, you have to first type
source activate phyin a terminal (omit the
sourceon Windows), and then call
Updating the software
To get the latest version of the software, open a terminal and type:
source activate phy # omit the `source` on Windows pip install phy phycontrib --upgrade
Installing the development version
You first need to download and install git. Then, use the regular command line terminal (not the git shell) and type the following:
source activate phy # omit the `source` on Windows pip install git+https://github.com/kwikteam/phy git+https://github.com/kwikteam/phy-contrib --upgrade
- User documentation of the Template GUI
- Developer documentation (work in progress)
- Mailing list
- Sample data repository (work in progress)