fastspt 16.1

A library to perform kinetic modeling of fast single particle tracking experiments

Spot-On (cli)

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.

Dependencies

• numpy
• scipy
• lmfit

Optional: jupyter

Your package manager may provide precompiled versions of numpy and scipy. In that case, it might be worth using those libraries, because compilation can take a significant amount of time.

Installation (from pip)

pip install fastspt

Installation (from this Gitlab) repository

Install dependencies

pip install -r requirements.txt

Alternatively, you can install the dependencies manually by typing: pip install numpy scipy lmfit

Optional : pip install jupyter

Install fastSPT

Simply run (as root): python setup.py install

Check that it worked: python -c "import fastspt"

Tutorial

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

Usage

Main functions

Extra functions

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.

Input file format

Caveats

References

License

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/>.

Deploying (developer only)

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

Authors

Maxime Woringer, Anders Sejr Hansen

Bugs/suggestions

Send to bugtracker or to email.