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While tracking objects is not rocket science the accuracy of your results depends heavily on the quality of your data and excessive optimization of the imaging process might be needed to ensure that the data is usable. The faster the particles move the more often you need to take pictures.  You also have to consider why your sample is moving and why you expect to see a difference in the speeds.  Cells that have no reason to move are likely to stay in place or move in a random fashion. If you want to study cell motility, a wound healing assay should be considered. 

Imaris has a good tool set for both automatic and manual tracking of moving objects thought the results given by the automatic algorithm should be scrutinized carefully and the parametrization has to be carefully reviewed so that it matches the data as well as possible.  Imaris can be found on 3D workstation, LS workstation and HELMI 3D workstation.