Strain mapping of heterogeneous biological tissues with MATLAB.

##Dependencies

• MATLAB 7 or later. MATLAB Image Processing Toolbox.
• 'Digital Image Correlation & Tracking with Matlab' - Digital Image Correlation & Tracking with MATLAB

##Usage

This project is really just a collection of functions that are built to work with the 'Digital Image Correlation & Tracking' package, linked above. The DIC package is really powerful and customizable, and it has it's own readme. You should check out the DIC readme for help with the specific functions.

There are three parts to making a typical measurement of strains in an image. Steps 1-3 correspond to functions found in the DIC package linked above - step 4 corresponds to scripts in this folder.

1. filelist_generator.m Build a file name list, which is just an ordered list of the images you want to analyze, and save them to filenamelist.mat.
2. grid_generator.m Select a grid of points to track from image to image. These are saved in .mat files called grid_x.mat and grid_y.mat. You can read the DIC readme for for information about these data structures. long story short - grid_x and grid_y are just arrays of the initial x- and y-coordinates of each gridpoint.
3. automate_image.m Track the position of those gridpoints from one image to the next. These displacements are saved in validx.dat and validy.dat.
4. strain_XXX.m There are a number of different scripts that follow this convention, and that's because they all do basically the same thing. They calculate various strains, from the displacements calculated in step 3. They are slightly different - they use different numerical approximations for the derivatives, for example. You can use them as guidelines for writing your own strain measurement script.

##Testing Your Implementation

In order to lend confidence to your results, you might want to generate some test images where you decide the exact deformations that take place. Check out the example test images generated by performing a simple Affine Transformation, in the subdirectory Strain Map Testing. There are also some example scripts which might be helpful for making your own test images, relevant to the types of deformations you are trying to measure. The script StrainError.m might be useful as a template for quantifying the error in test images.