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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. The standard version of Stimfit 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. The "lite" version of Stimfit comes without an embedded Python shell. Stimfit-lite is more lite-weight, easier to build and install. Stimfit is using the Import filters of Biosig which supports reading of over 50 different dataformats.

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

GNU/Linux

Debian-based systems (incl Ubuntu, and on WSL2)

you can get Stimfit and the stfio module from the standard repositories:

$ sudo apt-get install stimfit python-stfio

This approach works also on WSL2 of the most recent version of Windows10 (build: 10.0.19045.2546 ). Stimfit is also available through a number of distros

MacOSX:

MacPorts

$ sudo port install stimfit py27-stfio

Homebrew: stimfit (lite, no embedded Python)

  • Stimfit-lite (w/o python) can be also installed through HomeBrew. Afer installing homebrew, run
$ brew install schloegl/biosig/stimfit

MS-Windows:

There are several options to install Stimfit on Windows. Each has its own advantages (+) and disadvantages (-):

The traditional version of Stimfit v0.15.8-beta1

including the python-stfio module, is available from releases. It is quite dated, there are a number of known issues with import filters.

 - import filter not up-to-date [issues: 93, 95, 97]
   affected formats: ABF2, ATF, AXG, CNT, EDF+, HEKA, IBW, MFER, RHD/RDS
 - python2 only, python2 has reached end-of-live, (issue 88)
 - warning from windows defender (issue 98 [3])
 + works with all versions of Windows7 and later.

Stimfit lite v0.16.2

The lite-version of Stimfit (w/o embedded Python) is available as part of the Biosig-tools. Download, unzip and copy ../bin/stimfit.exe to your desktop.

 + import filters are up-to-date (chances are this would address the issues: 93, 95, 97 [3]).
 - no embedded python (CLI, printing not available)
 - warning from windows defender (issue 98 [3])
 + works with all versions of Windows7 and later.

Stimfit through WSL2

With the most recent version of Windows10 (build: 10.0.19045.2546 ), Stimfit for Linux can be installed through WSL2. e.g. when using Ubuntu in WSL2 (see GNU/Linux above).

 + import filters are up-to-date
 + python3 embedded
 + no warnings from windows defender, checksum of download is checked by "apt"
 - requires most recent Windows10 (version 10.0.19045.2546) with WSL2; certain functionality (e.g. copy/paste, file access) might require a non-standard workflow.

From Source

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.