2D

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

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This plugin permit to measure the signal spread of a molecule with respect to the cell area.

This plugin comes with Fiji

This plugin can be used to estimate nonlinear distortions induced by the image acquisition process[1] . It does not require special calibration samples, but needs sufficient overlapping image areas with preferably high contrast. For further information on how to best arrange calibration images please see the documentation.

2D Image registration method based on elastic deformations represented by B-splines.

An ImageJ plugin for manually tracking objects by mouse clicking. 

This plugin is bundled with Fiji.