Semi-elastic fiber optimisation in python.
Project description
SAENOPY: 3D Traction Force Microscopy with Python
SAENOPY is a free open source 3D traction force microscopy (TFM) software. Its material model is especially well suited for tissue-mimicking and typically highly non-linear biopolymer matrices such as collagen, fibrin, or Matrigel.
It features a python package to use in scripts and an extensive graphical user interface.
Check out our Documentation on how to install and use it.
Installation
Standalone
To use saenopy without a complicated installation you can use our standalone binaries to get started right away.
Windows https://github.com/rgerum/saenopy/releases/download/v1.0.8/saenopy.exe
Linux https://github.com/rgerum/saenopy/releases/download/v1.0.8/saenopy
MacOS https://github.com/rgerum/saenopy/releases/download/v1.0.8/saenopy_mac.app.zip (in development..)
Using Python
If you are experienced with python or even want to use our Python API, you need to install saenopy as a python package. Saenopy can be installed directly using pip:
``pip install saenopy``
Now you can start the user interface with:
``saenopy``
Or by executing the script “gui_master.py” in your python interpreter.
Getting started
To get started you can have a look at our collection of example datasets.
Preprint
If you want to cite saenopy you can reference our article:
Dynamic traction force measurements of migrating immune cells in 3D biopolymer matrices
David Böhringer, Mar Cóndor, Lars Bischof, Tina Czerwinski, Niklas Gampl, Phuong Anh Ngo, Andreas Bauer,
Caroline Voskens, Rocío López-Posadas, Kristian Franze, Silvia Budday, Christoph Mark, Ben Fabry, Richard Gerum
Nat. Phys. 20, 1816–1823 (2024); doi: https://doi.org/10.1038/s41567-024-02632-8
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