My ImageJ Plugins
Implementing the template matching function from the OpenCV library
Align (register) slices within an image stack (time lapse movie) via a user specified landmark

Iterative PIV using conventional cross-correlation or normalized correlation coefficient

Pick up the slice/slices with best focus quality using a modified normalized variance method
Fourier Transform traction cytometry (FTTC) method to calculate the traction force from displacement field

Use the FFMPEG library to save your image stack as Quicktime movie (mov), windows media (avi, wmv), MPEG4, Flash movie (FLV)

The adaptive threshold (local threshold) method with live preview