fabrylab/pytfm

2 dimensional particle image velocimetry, traction force microscopy and monolayer stress microscopy

Readme

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.

pytfm's Issues

Numpy 1.24.2 fails the pyTFM add-on

One of the files in the older openpiv version you use has np.float and this fails with the new numpy > 1.24

one workaround we found was to uninstall the default numpy and reinstall it

pip uninstall numpy
pip install numpy"<1.24"

A better solution is to update your use to a more recent version of openpiv-python which resolved this problem long ago.

Question about units for stress tensor

Hello!

Thanks for uploading your code to github. This is not really an issue but more of a question. My name is Vivek Gupta, I'm a graduate student who was using your code. I used the example included in your python tutorial. The traction stresses from your code are outputting reasonable data. However, when I run the the monolayer stress microscopy the stress values I am seeing are on the order of 10^-8 Pa. I noticed when you calculate the mean stress you divide by the pixel size and 10^-6, which essentially gives stress values on the order of 10^-2 Pa, which are still very little. So I'm assuming I'm mis-interpretting the units somwhere. Would you be able to clarify? Or if the values you get are not what I mentioned above, what should the values be? I am not too familiar with coding in general, and Python as well, so just want to double check if I'm doing everything correctly.

Thanks for your your help.

Best,
Vivek

shall we inform you on changes to openpiv?

Hi,

we've updated to 0.23.6 that should work out of box. it has some important fix in the filters, especially for cases with different magnitudes of u,v, components.

I could realize that we break sometimes your software, so I'd like to see if it's something we can regulate better.

Regards
Alex

No module named 'TFM_addon.TFM_addon'; 'TFM_addon' is not a package

After much trial and error clickpoints was successfully installed. After pip installing pyTFM and opening click points, I went to import the pyTFM addon and received the error in the title.

import add-on path C:\Users\MECHANO3BIOLOGY Lab\AppData\Local\Programs\Python\Python311\Lib\site-packages\pyTFM
import TFM_addon.TFM_addon
Traceback (most recent call last):
  File "C:\Users\MECHANO3BIOLOGY Lab\AppData\Local\Programs\Python\Python311\Lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 420, in add_script
    self.script_launcher.activateScript(self.selected_script)
  File "C:\Users\MECHANO3BIOLOGY Lab\AppData\Local\Programs\Python\Python311\Lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 501, in activateScript
    if script.activate(self, silent=silent):
       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\MECHANO3BIOLOGY Lab\AppData\Local\Programs\Python\Python311\Lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 230, in activate
    raise err
  File "C:\Users\MECHANO3BIOLOGY Lab\AppData\Local\Programs\Python\Python311\Lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 224, in activate
    self.addon_module = import_module(folder + "." + basefilename)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\MECHANO3BIOLOGY Lab\AppData\Local\Programs\Python\Python311\Lib\importlib\__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1135, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'TFM_addon.TFM_addon'; 'TFM_addon' is not a package

resolution has not been found