Semi-automated

Description

Compute and display the histogram of a sequence, with a more accurate control on the histogram parameters (such as the number of bins) than the built-in Icy widget. In particular, the histogram can be computed either over a whole sequence or over a sub-region defined by a ROI.

has function
Description

FlowJ is a collection of popular 2D optical flow algorithms, Lucas and Kanade, Uras, Fleet and Jepson, and Singh, in Java.

Bundled with Fiji, but can also be simply installed to ImageJ as well.

has function
Description

The plugin Landmark Correspondences calculates a transformation between two corresponding landmark clouds and renders a transformed image. The landmarks are read from point selections over two images. The transformation is estimated by a least squares or Moving Least Squares fit for the available models.

Description

TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation (Fiji comes with TrakEM2). It supports arbitrary-sized datasets. 

Menu of TrakEM2