Building Stimfit¶
- Author:
Alois Schlögl, Jose Guzman, Christoph Schmidt-Hieber
- Date:
02 April, 2026
This document describes how to install Stimfit dev under GNU/Linux. The installation was tested on Debian 10 (Buster) and 11 (Bullseye) with support for Python 3.*. It should work on other Debian-based systems (e.g. Ubuntu) as with newer version of Stimfit as well. I assume that you have the GNU C compiler (gcc) and the GNU C++ compiler (g++) and that both versions match.
Important
The historical autotools build described in older Stimfit documentation is no longer the supported path for current [master](README.md:13). Use the CMake workflow from [BUILDING.md](BUILDING.md) or the commands below.
What we need before we start¶
For the impatient, here are all Stimfit build dependencies : for Debian13/bookworm (and probably Ubuntu 24.xx) and later
$ sudo apt-get install \
python3-dev \
python3-numpy \
python3-matplotlib \
libhdf5-dev \
swig \
sip-tools \
python3-wxgtk4.0 \
libwxgtk3.2-dev \
wx-common \
libfftw3-dev \
libbiosig-dev \
liblapack-dev \
chrpath \
git \
automake \
autoconf \
libtool \
libgtest-dev
for Debian11/bullseye (and probably Ubuntu 20.x) it was
$ sudo apt-get install \
python3-dev \
python3-numpy \
python3-matplotlib \
libhdf5-serial-dev \
swig \
python3-sip-dev \
python3-wxgtk4.0 \
libwxgtk3.0-gtk3-dev \
wx-common \
libfftw3-dev \
libbiosig-dev \
liblapack-dev \
chrpath \
git \
automake \
autoconf \
libtool \
libgtest-dev
This will get you, amongst others:
[wxWidgets]: C++ graphical user interface toolkit (version >= 2.8; tested with 3.2.8, 3.3.1)
[wxPython]: GUI toolkit for the Python language.
[boost]: C++ library that is mainly used for its shared pointers (only needed when -std=c++17 is not supported)
[Biosig]: A library for reading a large number biomedical signal data formats.
[Lapack]: A linear algebra library.
[fftw]: Library for computing Fourier transformations.
[NumPy]: To handle numerical computations with Python (tested with version >=1.19).
[HDF5]: Hierarchical Data Format 5 (HDF5) to manage large amount of data.
[Matplotlib]: Plotting library for Python (use version >= 1.5.1)
In addition, install Sphinx and Doxygen if you want to build the documentation.
Optional: PyEMF¶
[PyEMF] is needed to export figures to the windows meta file format (WMF/EMF). EMF is a vector graphics format and can be imported in different Office software including LibreOffice. To install it, do:
$ wget http://sourceforge.net/projects/pyemf/files/pyemf/2.0.0/pyemf-2.0.0.tar.gz/download -O pyemf-2.0.0.tar.gz
$ tar xvf pyemf-2.0.0.tar.gz && cd pyemf-2.0.0
$ sudo python setup.py install
Download the Stimfit source code¶
You can download the latest development code for Stimfit from the Github code repository. For that, type from your current $HOME directory:
$ git clone https://github.com/neurodroid/stimfit.git
This will grab all the required files into $HOME/stimfit. If you’d like to update at a later point, do:
$ cd $HOME/stimfit
$ git pull
Build Stimfit¶
Go to the stimfit directory (in our example $HOME/stimfit) and configure a dedicated CMake build directory:
$ cd $HOME/stimfit
$ cmake -S . -B build/linux -G Ninja \
-DCMAKE_BUILD_TYPE=Release \
-DSTF_ENABLE_PYTHON=ON \
-DSTF_WITH_BIOSIG=ON
$ cmake --build build/linux --parallel
$ sudo cmake --install build/linux
Note
If you want to install Stimfit as a local user into ~/.local or target a specific Python interpreter, add the relevant CMake cache entries during configure, for example:
$ cmake -S . -B build/linux-local -G Ninja \
-DCMAKE_INSTALL_PREFIX=$HOME/.local \
-DPython3_EXECUTABLE=$HOME/.local/bin/python3
Then run `cmake --build` and `cmake --install` as your normal user.
Building Stimfit with BioSig import filter¶
We recommend to build Stimfit with the BioSig library to import files in from different biomedical disciplines. It is necessary to read files acquired with HEKA amplifiers or with Signal from CED. To do it, follow this instructions:
Install libbiosig-dev through the package manager of your distribution:
sudo apt-get install libbiosig-dev
Alternatively, use the in-tree BioSig provider managed by the current CMake toolchain. This is the preferred fallback when your distribution package is too old or unavailable:
$ cd $HOME/stimfit
$ cmake -S . -B build/linux-biosig-submodule -G Ninja \
-DCMAKE_BUILD_TYPE=Release \
-DSTF_WITH_BIOSIG=ON \
-DSTF_BIOSIG_PROVIDER=SUBMODULE
$ cmake --build build/linux-biosig-submodule --parallel
Alternatively, if you are maintaining BioSig itself and need a separate local checkout from its git repository:
sudo apt-get install libsuitesparse-dev libz-dev gawk libdcmtk-dev
git clone https://git.code.sf.net/p/biosig/code biosig-code
cd biosig-code
Then build that checkout using the current BioSig project’s own documented build instructions, install it into your desired prefix, and point Stimfit’s CMake configure step at that installation through the appropriate provider settings.
After that you can configure Stimfit with -DSTF_WITH_BIOSIG=ON and, when needed, select the desired provider through -DSTF_BIOSIG_PROVIDER=….
Building documentation¶
The manual of Stimfit is published at https://neurodroid.github.io/stimfit/. For a local build, install Sphinx and related helpers in a Python 3 environment:
python3 -m pip install -r doc/sphinx/requirements.txt sphinx
To build a local copy call:
sphinx-build -b html doc/sphinx doc/sphinx/.build/html
The HTML documentation will be written to doc/sphinx/.build/html/index.html.
Additionally, the source code can be documented with [Doxygen]. Install Doxygen and Graphviz first:
sudo apt-get install doxygen graphviz
Enter a directory called doc inside Stimfit (e.g $HOME/stimfit/doc) and type:
cd $HOME/stimfit/doc
doxygen Doxyfile.in
The local documentation of the source code will be in $HOME/stimfit/doc/doxygen/html.
