neurodroid / stimfit

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. Branch model The repository uses two upstream lines and two Debian packaging lines: • : primary development branch for the modern CMake-based toolchain • : legacy-maintenance branch for the historical 0.16/autotools line • : Debian unstable packaging branch tracking • : Debian packaging branch tracking Contributor and maintainer workflow details are documented in BRANCHES.md. 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: 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 Homebrew: stimfit (lite, no embedded Python) • Stimfit-lite (w/o python) can be also installed through HomeBrew. Afer installing homebrew, run 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. 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. 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). From Source • Build guide for GNU/Linux • Build guides for MacOSX • Build guides for Windows • Cross-compiling Stimfit with MXE on GNU/Linux for Windows Windows installer packaging (CMake + CPack) The CMake build can produce a distributable Windows installer with CPack. Prerequisites: • Inno Setup 6 installed (for the CPack generator) • Visual Studio 2022 build tools • Python environment matching the selected configure preset when embedded Python is enabled Example workflow for a Python-enabled Windows release build: The resulting artifacts are written into the build directory and include: • an Inno Setup installer executable • a ZIP fallback package from the same install tree Important links • Online documentation • User mailing list • Downloads 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. Build system migration status An initial CMake bootstrap layer is available to support migration from Autotools. See for details.