Welcome to the SAENOPY Documentation

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.

This migration immune cell demonstrated what scientific discoveries you can achieve with saenop:

Contents

• Interface
  • Interface Solver
• Boundary Condition Mode
  • Theory
  • Example
• Regularization Mode
  • Theory
  • Example
• Mesh
  • Mesh definition
  • Defining Inputs
• Material
  • Semi-Affine Fibers
  • Materials
  • Defining custom materials
  • Macrorheology
  • Fitting material parameters
• Examples
• API
  • Solver

Installation

Standalone

You can download saenopy as a standalone application for windows or for linux:

Windows https://github.com/rgerum/saenopy/releases/download/v1.0.2/saenopy.exe

Linux https://github.com/rgerum/saenopy/releases/download/v1.0.2/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

Citing Saenopy

If you use Saenopy for academic research, you are highly encouraged (though not required) to cite 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

You can also refer to the previous publications on the predecessor of saenopy:

• Steinwachs J., Metzner C., Skodzek K., Lang N., Thievessen I., Mark C., Munster S., Aifantis K. E., Fabry B. (2016) “Three-dimensional force microscopy of cells in biopolymer networks”. In Nat Methods, volume 13, 2016. doi.org/10.1038/nmeth.3685

• Condor M., Steinwachs J., Mark C., Garcia-Aznar J. M., Fabry B. (2017) “Traction Force Microscopy in 3-Dimensional Extracellular Matrix Networks” In Curr Protoc Cell Biol, volume 75, doi.org/10.1002/cpcb.24