.. saenopy documentation master file

Welcome to the SAENOPY Documentation
====================================

.. figure:: images/Logo.png


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 userinferface also has
integrations for spheriods, fiber alignment and 2D traction force microscopy.

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

.. raw:: html

    <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden; max-width: 100%; height: auto;">
        <iframe src="//www.youtube.com/embed/g7vlqs_hT4s" frameborder="0" allowfullscreen style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"></iframe>
    </div>
    <br/>

.. toctree::
   :caption: Contents
   :maxdepth: 2

   interface
   boundarycondition.ipynb
   regularization.ipynb
   mesh
   material.ipynb
   auto_examples/index.rst
   ReadInData
   api

Installation
------------

Standalone
~~~~~~~~~~
You can download saenopy as a standalone application:

Windows
https://github.com/rgerum/saenopy/releases/download/v1.0.6/saenopy.exe

Linux
https://github.com/rgerum/saenopy/releases/download/v1.0.6/saenopy

MacOS
https://github.com/rgerum/saenopy/releases/download/v1.0.6/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``

Integrations
------------

Aside from saenopy's main use or 3D traction force microscopy we provide in our interface
integrations to related methods to asses 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" <https://doi.org/10.7554/eLife.51912>`_.
   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" <https://doi.org/10.1016/j.matbio.2023.11.004>`_.
  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" <https://doi.org/10.1371/journal.pcbi.1008364>`_.
  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" <https://doi.org/10.1038/s41567-024-02632-8>`_.
  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" <http://dx.doi.org/10.1038/nmeth.3685>`_.
  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" <http://dx.doi.org/10.1002/cpcb.24>`_
  In Curr Protoc Cell Biol, volume 75, doi.org/10.1002/cpcb.24