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. The user interface also has integrations for spheroids, fiber alignment and 2D traction force microscopy.

This migrating immune cell demonstrates what scientific discoveries you can achieve with saenopy:

Contents

3D TFM
- Interface
- Parameters
- Theory
- Examples
- API
2.5D Spheroid
- Theory
- Interface
- Parameters
- API
2.5D Orientation
- Theory
- Interface
- Parameters
- API

Installation¶

Standalone¶

You can download saenopy as a standalone application. These links always resolve to the newest release, so they do not need to be updated here when a new version is published:

Windows: saenopy.exe
Linux: saenopy
MacOS: saenopy_mac.app.zip (in development)

All releases are listed on the releases page.

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

Integrations¶

Aside from saenopy’s main use for 3D traction force microscopy, our interface provides integrations of related methods to assess cellular forces.

Spheroid¶

3D traction force microscopy on multicellular aggregates (so-called spheroids).

https://github.com/christophmark/jointforces

Mark C., Grundy T., Strissel P., Böhringer D., Grummel N., Gerum R., Steinwachs J., Hack C., Beckmann M., Eckstein M., Strick R., O’Neill G., Fabry B. (2020). “Collective forces of tumor spheroids in three-dimensional biopolymer networks”. In eLife 9:e51912. doi.org/10.7554/eLife.51912

Orientation¶

Use fiber alignment as a proxy for force if the material properties are not available.

https://github.com/davidbhr/CompactionAnalyzer

Böhringer D., Bauer A., Moravec I., Bischof L., Kah D., Mark C., Grundy T.J., Görlach E., O’Neill G.M., Budday S. and Strissel P.L., (2023). “Fiber alignment in 3D collagen networks as a biophysical marker for cell contractility”. Matrix Biology, 124, pp.39-48. doi.org/10.1016/j.matbio.2023.11.004

pyTFM¶

Analyze force generation and stresses in cell colonies and confluent cell layers growing on a 2 dimensional surface.

https://github.com/fabrylab/pyTFM

Bauer A., Prechová M., Fischer L., Thievessen I., Gregor M., & Fabry B. (2021). “pyTFM: A tool for traction force and monolayer stress microscopy”. PLoS computational biology, 17(6), e1008364. doi.org/10.1371/journal.pcbi.1008364

Citing Saenopy¶

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

Böhringer D., Cóndor M., Bischof L., Czerwinski T., Gampl N., Ngo P.A., Bauer A., Voskens C., López-Posadas R., Franze K., Budday S., Mark C., Fabry B., Gerum R. (2024). “Dynamic traction force measurements of migrating immune cells in 3D biopolymer matrices”. Nat. Phys., 20, 1816–1823 (2024). doi.org/10.1038/s41567-024-02632-8

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