Metadata-Version: 2.1
Name: phy
Version: 2.0b5
Summary: Interactive visualization and manual spike sorting of large-scale ephys data
Home-page: https://phy.cortexlab.net
Author: Cyrille Rossant (cortex-lab/UCL/IBL)
Author-email: cyrille.rossant+pypi@gmail.com
License: BSD
Description: # phy: interactive visualization and manual spike sorting of large-scale ephys data
        
        [![Build Status](https://travis-ci.org/cortex-lab/phy.svg)](https://travis-ci.org/cortex-lab/phy)
        [![codecov.io](https://img.shields.io/codecov/c/github/cortex-lab/phy.svg)](http://codecov.io/github/cortex-lab/phy)
        [![Documentation Status](https://readthedocs.org/projects/phy/badge/?version=latest)](https://phy.readthedocs.io/en/latest/?badge=latest)
        [![GitHub release](https://img.shields.io/github/release/cortex-lab/phy.svg)](https://github.com/cortex-lab/phy/releases/latest)
        [![PyPI release](https://img.shields.io/pypi/v/phy.svg)](https://pypi.python.org/pypi/phy)
        
        
        [**phy**](https://github.com/cortex-lab/phy) is an open-source Python library providing a graphical user interface for visualization and manual curation of large-scale electrophysiological data. It is optimized for high-density multielectrode arrays containing hundreds to thousands of recording sites (mostly [Neuropixels probes](https://www.ucl.ac.uk/neuropixels/)).
        
        Phy provides two GUIs:
        
        * **Template GUI** (recommanded): for datasets sorted with KiloSort and Spyking Circus,
        * **Kwik GUI** (legacy): for datasets sorted with klusta and klustakwik2.
        
        
        [![phy 2.0b1 screenshot](https://user-images.githubusercontent.com/1942359/74028054-c284b880-49a9-11ea-8815-1b7e727a8644.png)](https://user-images.githubusercontent.com/1942359/74028054-c284b880-49a9-11ea-8815-1b7e727a8644.png)
        
        
        ## What's new
        
        * [7 Feb 2020] Release of phy 2.0 beta 1, with many new views, new features, various improvements and bug fixes...
        
        
        ## Links
        
        * [Documentation](http://phy.readthedocs.org/en/latest/)
        * [Mailing list](https://groups.google.com/forum/#!forum/phy-users)
        
        
        ## Installation instructions
        
        Phy requires a recent GPU and an SSD for storing your data (the GUI may be slow if the data is on an HDD).
        
        1. Install the latest version of [Anaconda 64-bit with Python 3](https://www.anaconda.com/distribution/#download-section).
        
        2. Open a terminal and type:
        
        ```bash
        conda create -n phy2 python=3.7 pip numpy matplotlib scipy scikit-learn h5py pyqt cython pillow -y
        conda activate phy2
        pip install phy --pre --upgrade
        # Only if you plan to use the Kwik GUI:
        # pip install klusta klustakwik2
        ```
        
        3. Phy should now be installed. Open the GUI on a dataset as follows (the phy2 environment should still be activated):
        
        ```bash
        cd path/to/my/spikesorting/output
        phy template-gui params.py
        ```
        
        ### Dealing with the error `ModuleNotFoundError: No module named 'PyQt5.QtWebEngineWidget`
        
        In some environments, you might get an error message related to QtWebEngineWidget. Run the command `pip install PyQtWebEngine` and try launching phy again. This command should not run if the error message doesn't appear, as it could break the PyQt5 installation.
        
        
        ### Upgrading from phy 1 to phy 2
        
        * Do not install phy 1 and phy 2 in the same conda environment.
        * It is recommended to delete `~/.phy/*GUI/state.json` when upgrading.
        
        
        ### Developer instructions
        
        To install the development version of phy in a fresh environment, do:
        
        ```bash
        git clone git@github.com:cortex-lab/phy.git
        cd phy
        pip install -r requirements.txt
        pip install -r requirements-dev.txt
        pip install -e .
        cd ..
        git clone git@github.com:cortex-lab/phylib.git
        cd phylib
        pip install -e . --upgrade
        ```
        
        ### Troubleshooting
        
        * [See a list of common issues.](https://phy.readthedocs.io/en/latest/troubleshooting/)
        * [Raise a GitHub issue.](https://github.com/cortex-lab/phy/issues)
        
        
        ## Running phy from a Python script
        
        In addition to launching phy from the terminal with the `phy` command, you can also launch it from a Python script or an IPython terminal. This may be useful when debugging or profiling. Here's a code example to copy-paste in a new `launch.py` text file within your data directory:
        
        ```
        from phy.apps.template import template_gui
        template_gui("params.py")
        ```
        
        
        ## Credits
        
        **phy** is developed and maintained by [Cyrille Rossant](http://cyrille.rossant.net).
        
        * [International Brain Laboratory](https://internationalbrainlab.org)
        * [Cortex Lab (UCL)](https://www.ucl.ac.uk/cortexlab/) ([Kenneth Harris](https://www.ucl.ac.uk/biosciences/people/harris-kenneth) and [Matteo Carandini](https://www.carandinilab.net/)).
        
        Contributors to the repository are:
        
        * [Alessio Buccino](https://github.com/alejoe91)
        * [Michael Economo](https://github.com/mswallac)
        * [Cedric Gestes](https://github.com/cgestes)
        * [Dan Goodman](http://thesamovar.net/)
        * [Max Hunter](https://iris.ucl.ac.uk/iris/browse/profile?upi=MLDHU99)
        * [Shabnam Kadir](https://iris.ucl.ac.uk/iris/browse/profile?upi=SKADI56)
        * [Christopher Nolan](https://github.com/crnolan)
        * [Martin Spacek](http://mspacek.github.io/)
        * [Nick Steinmetz](http://www.nicksteinmetz.com/)
        
Keywords: phy,data analysis,electrophysiology,neuroscience
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Framework :: IPython
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
