pyTFM is a python package that allows you to analyze force generation and stresses in 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.
Please refer to the Documentation of pyTFM for detailed instructions on installation and usage.
You need to create python 3.6 enviroment.
conda create --name pyTFM python=3.6
conda activate pyTFM
Note: python 3.7 works too, but clickpoints need python 3.6.
pyTFM package install
pip install git+https://github.com/fabrylab/pyTFM.git
If you want to use jupyterlab
pip install jupyterlab
jupyter-lab
Sometimes it is necessary to reinstall pyTFM again through the JupyterLab because of scikit-image package.