Welcome to pyTFM’s documentation!

pyTFM is a python package that allows you to analyze force generation and stresses in cells, cell colonies and confluent cell layers growing on a 2 dimensional surface. This package implements the procedures of Traction Force Microscopy and Monolayer Stress Microscopy. In addition to the standard measures for stress and force generation, it also includes the line tension, a measure for the force transfer exclusively across cell-cell boundaries. pyTFM includes an addon for the image annotation tool clickpoints allowing you to quickly analyze and vizualize large datasets.

Contents:

• Installation
  • Dependencies
• Introduction to Traction Force Microscopy and Monolayer Stress Microscopy
• Tutorials
  • Analyzing Cell Colonies with Clickpoints
  • Using pyTFM in Python
• Typical Measures for Force Generation and Stresses in Cells
  • Deformations in the Substrate
  • Strain Energy
  • Contractility
  • Average Normal and Shear Stress
  • Distribution of Stresses
  • Forces acting across Cell Boundaries
• Using Config Files, Hidden Parameters and Plotting Behavior
  • Hidden Parameters
  • Using Config Files
  • Overview of Analysis Parameters
  • Overview of Plotting Parameters

Note

If you encounter any bugs or other problems please report them here or contact me at andreas.b.bauer@fau.de.