This repository collects a series of scripts to analyze data from single particle tracking experiments. The code was initially written by Anders Sejr Hansen and translated to Python by Maxime Woringer. A Matlab version exists and is maintained by Anders Sejr Hansen.
This repository only includes the commandline analysis pipeline. A graphical user interface (GUI) is available for a more user-friendly analysis, but is not included in this repository. This repository contains the command-line version, that can be used independently from the GUI.
Although the functions and methods can be called directly, we provide a walk-through tutorial as a Jupyter notebook.
Use docker to get preconfigured jupyter lab instance.
docker build --rm -f "Dockerfile" -t spot-on-cli:lab-scipy .
docker run --rm -it -v c:\Users\andre:/home/jovian/andrey -p 8888:8888/tcp spot-on-cli:lab-scipy
See requirements.txt
pytest --cov fastspt --cov-report xml:cov.xml
git clone https://github.com/aaristov/Spot-On-Cli.git
pip install .
pip install -r requirements.txt
Alternatively, you can install the dependencies manually by typing:
pip install numpy scipy lmfit
Optional : pip install jupyter
Simply run (as root): python setup.py install
Check that it worked: python -c "import fastspt"
A short tutorial, demonstrating the capabilities of the software, is available as a Jupyter notebook.
See fastSPT_tutorial.ipynb. The tutorial is also available online: address of the page
Document here how to open a Jupyter notebook
The writers submodule contains some useful functions:
mat_to_csv(in_path, out_path)converts a .mat file to a CSV. It can easily be scripted.
This program is released under the GNU General Public License version 3 or upper (GPLv3+).
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
python setup.py sdist
gpg --detach-sign -a dist/fastspt-11.4.tar.gz
twine upload dist/fastspt-11.4.tar.gz dist/fastspt-11.4.tar.gz.asc
Maxime Woringer, Anders Sejr Hansen
Send to bugtracker or to email.