LD-3D-TFM

Large Deformation Traction Force Microscopy

This repositry contains the Matlab m-files to run our LD 3D TFM algorithm. The first part of the package includes the FIDVC algorithm, which is how the 3D displacement fields are calculated. The second part of the code package includes converting those displacement fields into 3D surface tractions as described in Toyjanova, Bar-Kochba et al., PloS One, 2014.

Depending on the geometry of the problem at hand, the included surface normal finder algorithm might need additional modification for traction calculation in fully embedded systems or on arbitrary geometries. Alternatively, the user can supply the his/her own point-by-point surface normals to calculate the surface tractions (e.g., Matlab has several already existing image processing options for extracting surface normals from rendered surfaces).

Important pages

Running 3D-VTFM

C Compiler

To run you need a compatible C compiler. Please see (http://www.mathworks.com/support/compilers/R2015a/index.html)

Input 3D Image Stack Requirements

To check if the 3D image stack have the required speckle pattern and intensity values for correlation please use our DVC simulator.
The 3D image stack need to be saved in a 3 dimensional matrix (intensity values are stored at x, y and z position) in vol.mat* files.
We recommend that the input image stack at each dimension should have at least 1.5 times of the subset size as the number of pixels. The default subset size is 128x128x64, so we recommend that the minimum input volume size should be 192x192x96.
The size of the input image stack should be divisible by 0.5 times the size of the subset.

Running included example case

Make sure that the main files and the supplemental m files (from file exchange) are added to the path in Matlab.
Download and save the example volume data in the example folder.
Run the exampleRunFile.m file

Health warning!

FIDVC in the 3D-VTFM requires a 3D stack to be read in, which depending on the volume size can require a large amount of RAM in Matlab.

Files

Main files

calculateNormals.m
calculateSurfaceUi.m
findSurface.m
fun3VDTFM.m
removeOutliers.m

Supplement m files from the MATLAB file exchange:

gridfit.m
inpaint_nans.m
inpaint_nans3.m

Example Run files

exampleRunFile.m
example volume data (vol00.mat, vol01.mat).

FAQ

What are the requirements for the input 3D image stack?

Please refer to input 3D Image Stack Requirements.

Cite

If used please cite: Toyjanova J., Bar-Kochba E., López-Fagundo C., Reichner J., Hoffman-Kim D, Franck, C. (2014) High Resolution, Large Deformation 3D Traction Force Microscopy. PLoS ONE 9(4): e90976. doi:10.1371/journal.pone.0090976

@article{toyjanova2014high,
  title={High resolution, large deformation 3D traction force microscopy},
  author={Toyjanova, Jennet and Bar-Kochba, Eyal and Lopez-Fagundo, Cristina and Reichner, Jonathan and Hoffman-Kim, Diane and Franck, Christian},
  journal={PloS one},
  volume={9},
  number={4},
  pages={e90976},
  year={2014},
  publisher={Public Library of Science}
}
}

Contact and support

For questions, please first refer to FAQ and Questions/Issues. Add a new question if similar issue hasn't been reported. We shall help you at the earliest. The author's contact information can be found at Franck Lab.

jyang526843 / LD-3D-TFM