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rgerum / saenopy

Semi-affine Elastic Network Optimizer to calculate forces in collagen or other biopolymer networks.
MIT License
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cell-mechanics collagen finite-element-methods modelling solver

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SAENOPY

DOC Coverage Status PyTest License: MIT

SAENOPY is a free open source 3D traction force microscopy 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 on Windows or Linux.

Windows https://github.com/rgerum/saenopy/releases/download/v1.0.5/saenopy.exe

Linux https://github.com/rgerum/saenopy/releases/download/v1.0.5/saenopy

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 preprint.

Dynamic traction force measurements of migrating immune cells in 3D matrices David Böhringer, Mar Cóndor, Lars Bischof, Tina Czerwinski, Andreas Bauer, Caroline Voskens, Silvia Budday, Christoph Mark, Ben Fabry, Richard Gerum bioRxiv 2022.11.16.516758; doi: https://doi.org/10.1101/2022.11.16.516758