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THIS REPOSITORY IS OUTDATED

The new repository can be found here.

Old notes

Spiky is the code name for the next-generation spike-sorting software adapted to high-channel count silicon probes. Written in Python, it aims at being flexible and extendable by the user.

The first step is to create a new semi-automatic graphical interface (code name: KlustaViewa) for the manual stage that comes after the automatic clustering algorithms. This interface automatically guides the user through similar clusters, showing the most relevant feature projections, and asks him or her to make merge or split decisions. The goal is to make the manual stage more reliable, less error-prone and quicker than what it currently is.

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

Installation

The software is still in development, but you can download an experimental version here.

Step 1

If you don't already have a Python distribution, install Enthought Python Distribution (EPD), which is free for academics (EPD ACADEMIC SUBSCRIPTION and NOT EPD FREE).

You need to click on request an academic license here on the webpage and create an account with your academic e-mail address.

Step 2

Download Spiky

Step 3

Extract this ZIP file in a temporary folder.

Step 4

  • On Windows, double-click on windows_install.bat.
  • On other systems, open a system shell in the temporary directory where you extracted the package, and execute the following command: python setup.py install.

Step 5

To run the software, execute spiky in a system shell.

On Windows, you may need to add C:\Python27\Scripts in the PATH variable, as described here.

Gallery

Screenshot 1 Screenshot 2 Screenshot 3

Installation for advanced users

Dependencies

The following libraries are required:

  • Python 2.7
  • Numpy
  • Pandas >= 0.10
  • Matplotlib >= 1.1.1
  • PyOpenGL >= 3.0.1
  • either PyQt4 or PySide

There are two possibilities to install these dependencies.

Use an all-in-one Python distribution

All these dependencies are included in the Enthought Python Distribution (EPD), which is free for academics.

Install all packages one by one

This solution can be useful if you already have a Python installation and only a few packages are missing.

  • On Windows, find the packages on this webpage.
  • On OS X, find them on Homebrew or Macports
  • On Ubuntu, use apt-get install with the appropriate package name, which you can find here:

    sudo apt-get install python-numpy python-pandas python-matplotlib python-opengl python-qt4 python-qt4-gl
    

Installer

Download Spiky, extract that package and execute python setup.py install.

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

    pip install -r requirements.txt
    
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