time-series

"This ImageJ plugin (CGE) is a semi-automatic tool to detect and track moving cell, and to measure the fluorescent protein expression level. CGE extracts the trajectory of the cells by tracking their displacements, makes the delineation of cell nucleus or whole cell, and finally yields measurements of various features, like reporter protein expression level, cell displacement."

This plugin stabilizes jittery image stacks using the Lucas-Kanade algorithm. It supports both grayscale and color images.

See also this tweet

An ImageJ plugin for manually tracking objects by mouse clicking. 

This plugin is bundled with Fiji.