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