Traction Force Microscopy

This package contains ImageJ plugins for the Traction Force Microscopy.

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-The first plugin is the iterative PIV by which you can get the displacement field from the bead images.

-The second plugin is the FTTC plugin that is used for reconstruct the force field from the displacement data.

-Both the FTTC and PIV plugins have a plot function that could help you visualize your displacement/force field

Source codes are available upon request. (qztseng /at/ gmail dot com)

Downloads

Download and install the PIV plugins first.

FTTC_.jar

Installation

(It is somehow complicated, please refer to the iterative PIV installation pages for more detailed instruction) :

1. Put the PIV_.jar , FTTC_.jar, javacv.jar , javacpp.jar , opencv.jar into your ImageJ plugins folder

2. Depending on your system architecture, put one of the following library files into your ImageJ plugins folder : 32-bit Windows , 64-bit Windows, 64-bit Mac, 32-bit Linux or 64-bit Linux

3. More detailed installation guide for OpenCV library

Short user guide

1. Two fluorescent bead images should be combined as an ImageJ stack, with the null force image( without cell) as the 1st slice and stressed image (with cell) as 2nd slice. 

2. You can do a pre-alignment to correct the experimental shift by using the Align slices in stack plugin, or any other slice registration plugin. 

3. The displacement field is calculated by the iterative PIV plugin. The best result is obtained by using the normalized correlation coefficient algorithm where the interrogation window is searched against a larger search window. But you need to have the OpenCV template matching plugin running correctly. Please refer to its installation guide.  

4. Otherwise, if you can't get the OpenCV template matching run correctly, you can choose to do PIV by conventional cross-correlation by setting the "search window size" equal to the "PIV window size". 

5. At the end of PIV run, you will be asked to save it or do further filtering operation. 

6. After obtaining the PIV data file, you can use the FTTC plugin to reconstruct the force field.

7. The reconstructed force field will be saved automatically at the same folder as the PIV file. (In some cases, ImageJ under Windows system might have access problem to other folders. If you have problem finding the automatically saved force field file, try to put your PIV file in a folder that ImageJ could access without problem, ex: Desktop\ or ImageJ\ )

8. The output force field is a text file with each column separated by space. The data is arranged as following:

x coordinate of the data (pixel) | y coordinate of the data (pixel) | x component of the traction force (pascal) | y component of the traction force (pascal) | force magnitude

9. The plot FTTC function can be used to plot both the force field as a color coded vector plot or a force magnitude stress map.

Remarks

• This TFM program is developed for my PhD work. I would like to thank my thesis supervisor Manuel Thery for letting me play around with the programing and not considering it as a waste of time (It is not at all the specialty in our lab).

• I would also like to thank Martial Balland for sharing his matlab FTTC code. 

• Thanks to Ulrich Schwarz and Benedikt Sabass for providing their matlab FTTC program for validating my force calculation result and read the Java code.

  • Thanks to Samuel Audet for his javacv library.

  • The FTTC package included the JAMA library from NIST and Mathworks as well as jTransforms library from Piotr Wendykier. If you have some old ImageJ plugins using an old version of jTransforms, you might get an error message like: java.lang.IllegalArgumentException: n1, n2 must be power of two numbers. This can be solved by just replacing the old jTransforms.jar with the latest version. 

Updates

• 2015/2/7: Updated javacv library files for PIV

• 2012/7/5: Force the reading of input file to use "." as decimal symbol and don't use any grouping symbol (i.e. "," in en_US locale) to avoid error parsing of number from input file for some system language environment  (ex: French ).

References

1. Tseng, Q. et al. Spatial Organization of the Extracellular Matrix Regulates Cell–cell Junction Positioning. PNAS (2012).doi:10.1073/pnas.1106377109

2. Tseng, Qingzong. 2011. “Study of multicellular architecture with controlled microenvironment”. Ph.D. dissertation, Université de Grenoble. https://tel.archives-ouvertes.fr/tel-00622264

Contact

        Please send comment to Qingzong Tseng (qztseng /at/ gmail dot com).

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