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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.

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.