THIS REPOSITORY IS OUTDATED
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.
The software is still in development, but you can download an experimental version here.
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.
Extract this ZIP file in a temporary folder.
- On Windows, double-click on
- 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.
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.
Installation for advanced users
The following libraries are required:
- Python 2.7
- 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 installwith 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
Download Spiky, extract that package
python setup.py install.
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
pipso that external packages are automatically updated (like
qtoolswhich contains some Qt-related utility functions):
pip install -r requirements.txt