Having acquired images for the purpose of tracking, the first task will be to establish an effective segmentation strategy. Several factors can complicate good segmentation throughout the time series. For example:

• The signal or background intensity may change throughout the time series.
• Objects coming into contact with other objects will need to be effectively separate.
• Object morphologies may change significantly throughout the time series resulting in the need for relatively permissive filters. 

All of these factors can, to some extent, be handled by image and object processing algorithms.