Welcome to the SAENOPY Documentation

SAENOPY a python implementation of the SAENO - Semi-affine Elastic Network Optimizer, originally developed by Julian Steinwachs.

Contents

• 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
  • Classic Single Cell TFM
  • Dynamical Single Cell TFM
• API

Installation

Saenopy can be installed directly using pip:

pip install saenopy

Citing Saenopy

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

• 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