Installing a Python distribution for KlustaViewa
This document gives the instructions to install a Python distribution with all dependencies required by the KlustaSuite.
All systems (Linux, Mac OS X, and Windows)
Important: do not use your OS package manager (like apt-get) nor pip to install Python and its main dependencies. Use Anaconda or Miniconda instead.
You can also download the Miniconda installer from a terminal:
Open a terminal in the directory where you downloaded Miniconda, and type the following command (the filename might be slightly different in your case). This will install Miniconda in your user account.
On Windows, you'll have to double-click on the
You'll be requested to answer a few questions.
Enterto review the license.
Spaceseveral times to scroll through the license.
- You'll be requested to choose the installation path. You can accept the default (
~/miniconda), so just type
- At the end of the installation, you'll be requested to choose whether this Python distribution should be the default one on your account. You can type
- Congratulations! Miniconda is now installed.
You may need to open a new terminal so that the
condacommand-line tool is available.
Type the following commands to install an isolated environment (named
klusta) of Python containing all the dependencies required by KlustaViewa. We also add extra, non-mandatory dependencies just in case you might need to compile KlustaViewa at some point. This will take several minutes because many packages will be automatically downloaded from the Internet. We specify specific versions for NumPy, pandas, and PyTables, because it has been reported that newer versions don't work with KlustaViewa.
conda create -n klusta python=2.7 --yes conda install -n klusta scipy pandas=0.12 pytables=3.0 pyqt setuptools pip cython nose ipython-notebook matplotlib --yes conda install -n klusta numpy=1.8 --yes
Now, activate your 'klusta' environment - you will need to do this before running any application.
source activate klusta
You currently have to use
pipto install the last dependency: PyOpenGL.
pip install pyopengl
Now, you can install the KlustaViewa package (that also contains SpikeDetekt) by following the instructions here (starting from (2)).
The following libraries are required:
- Python 2.7
- NumPy 1.8 (
- Pandas = 0.12 (
0.13 and laterwon't work)
- PyTables = 3.0
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
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.