It is my understanding that you want to calculate the direction of motion of cells in a video.
For this purpose, you may make use of optical flow techniques in Computer Vision. Optical flow techniques are usually used to estimate the apparent motion of objects, surfaces and edges in a visual scene. You may make use of the following link to get a high-level overview about the technique.
Regarding the implementation, you may use the estimateFlow function available in the Computer Vision toolbox. This function takes the video file and any one frame as input and returns an opticalFlow object. This contains information about the velocity, phase and amplitude components of the optical flow.
For detailed information on using estimateFlow function you may refer to the following link.
Hope this helps!
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