Estimating degree of motion in video frames
Probably you could try optical flow with some key-points not pixels if your purpose is to estimate motion. I thing meaningful thing would count average values of keypoints, overcomes some threshhold or filter (to eliminate barelly moving keypoints). However there would be some problems with having constant amount of meaningfull keypoints (keypoints tend to dissapear over time and very little chance that same amount newly generated keypoints are on moving objects). If that is what you want. You can estimate amplitudes of moving keypoints. 
Tools could be any CV library like OpenCV. Pixels are not easily trackable without being extracted as keypoints.

On the other hand if you want to estimate how much pixels moving on image and estimate movement results from codec movement compression you could extract frame by frame and ignore I type frames and count how much pixels are on B and P type frames (I am recalling from h264 not sure how these frames are expressed in vp8), which are just moving picture parts from previous/next frame. You then can have estimate how much pixels are moving. Your call how you will implement this.