jackieee / klustaviewa

GUI for spike sorting manual stage in Python

KlustaViewa

KlustaViewa is a software for semi-automatic spike sorting with high-channel count silicon probes. It streamlines the manual stage occurring after the automatic clustering stage by guiding the user through the clustered data, letting him or her refine the clusters. The goal is to make the manual stage more reliable, quicker, and less error-prone.

This software was developed by Cyrille Rossant in the Cortical Processing Laboratory at UCL.

User guide

• See the user guide here.

Screenshots

Note

You may encounter problems with the latest version of KlustaViewa if you have multiple shanks. You should put all *.1 files (+ the .xml file) in a separate folder before opening them in KlustaViewa. Idem for *.2 files, etc. The next version (to be released in a few weeks) will solve this problem.

Installation

• The software is in beta version at this time.
• It can run on Windows, Mac OS X and Linux.
• This document contains all the instructions to install the software on all systems.

Windows 7 & 8 (64 bits)

• Step 1: download the KlustaViewa Full Installer for Windows 64 bits (>200MB).
• Step 2: execute the installer.
• Step 3: click on the KlustaViewa icon on your desktop or in the Start menu to launch the software.
• Step 4: to update the software at any time, execute Update KlustaViewa in the Start menu (you need an active Internet connection).

Mac OS X and Linux

• Step 1: install Anaconda.

  • Download the adequate version (64 bits if possible).

  • Execute the installer. On Linux, you need to type a command similar to:

    $ bash Anaconda-1.6.1-Linux-x86_64.sh
    

  • You will need to press Enter or 'yes' at some steps.

• Step 2: execute the following commands:

  $ pip install pyopengl
  $ conda install -c http://conda.binstar.org/asmeurer pyside
  $ pip install klustaviewa
  

• Step 3: to run KlustaViewa, type the following command in a system shell:

  klustaviewa
  

Details

Dependencies

The following libraries are required:

• Python 2.7
• Numpy
• Pandas
• PyTables
• Matplotlib
• PyOpenGL
• either PyQt4 or PySide

OpenGL

KlustaViewa requires OpenGL >= 2.1. To find out which version of OpenGL is available on your system:

• Use OpenGL Extensions Viewer
• Alternatively, on Linux, run glxinfo.

KlustaViewa works better with a good graphics card as it uses hardware-accelerated visualization. With a lower end graphics card, the software will work but somewhat slower.

Development version

Use this if you want to be able to update with git pull (you need git).

• Clone the repository:

  git clone https://github.com/rossant/klustaviewa.git
  

• Install KlustaViewa with pip so that external packages are automatically updated (like qtools which contains some Qt-related utility functions):

  pip install -r requirements.txt
  

Contact

If you have any trouble, bug, comment or suggestion:

• You can send a message on the Google group.
• You can send an e-mail to the author of the software: cyrille dot rossant at gmail dot com.