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README.md

Stimfit

Documentation is available here.

Introduction

Stimfit is a free, fast and simple program for viewing and analyzing electrophysiological data. It's currently available for GNU/Linux, Mac OS X and Windows. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy. A standalone Python module for file i/o that doesn't depend on the graphical user interface is also available.

List of references

In this link you can find a list of publications that used Stimfit for analysis. We'd appreciate if you could cite the following publication when you use Stimfit for your research:

Guzman SJ, Schlögl A, Schmidt-Hieber C (2014) Stimfit: quantifying electrophysiological data with Python. Front Neuroinform doi: 10.3389/fninf.2014.00016

Installation

Windows

The Windows version, including the python-stfio module, is available here.

OS X

Stimfit for OS X is available through MacPorts. After installation of MacPorts, run

$ sudo port install stimfit py27-stfio

GNU/Linux

On Debian and Ubuntu systems, you can get Stimfit and the stfio module from the standard repositories:

$ sudo apt-get install stimfit python-stfio

More recent versions can be found on the Debian Neuroscience Repository, and there's a bleeding-edge ppa for Ubuntu on launchpad.

Important links

Source code structure

Directory Description
./src/libstfio File i/o library for common electrophysiology formats
./src/libstfnum Mathematical operations for measurements and fittings
./src/pystfio Python wrapper around libstfio
./src/stimfit Stimfit program
./src/stimfit/py stf module that gets imported into the embedded Python shell

libstfio is a private library that won't be installed system-wide. You may therefore end up with two copies of libstfio.so: One in the private stimfit library directory (/usr/lib/stimfit/ or similar), the other one in the Python site packages path for pystfio. libstfio may turn into a system-wide library in the future.

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