Documentation is available here.
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.
The repository uses two upstream lines and two Debian packaging lines:
master: primary development branch for the modern CMake-based toolchain0.16: legacy-maintenance branch for the historical 0.16/autotools linedebian/sid: Debian unstable packaging branch trackingmasterdebian/sid-0.16: Debian packaging branch tracking0.16
Contributor and maintainer workflow details are documented in BRANCHES.md.
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
For current source builds from this repository, use the CMake-based helper
scripts documented in BUILDING.md.
- Debian-based systems may provide
stimfitandpython-stfiopackages through their repositories. - Release artifacts for supported platforms are published on GitHub Releases.
- GNU/Linux build guide: https://neurodroid.github.io/stimfit/linux_install_guide/index.html
- macOS build guide: https://neurodroid.github.io/stimfit/osx_install_guide/index.html
- Windows build guide: https://neurodroid.github.io/stimfit/win_install_guide/index.html
The supported repository entry points are:
Windows packaging is performed with CMake and CPack through build_windows_msvc.ps1 as described in BUILDING.md.
| 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.
An initial CMake bootstrap layer is available to support migration from Autotools.
See CMAKE_MIGRATION.md for details.