Rigid registration

The ICP algorithm takes two point clouds as an input and return the rigid transformation (rotation matrix R and translation vector T), that best aligns the point clouds. Example: [R,T] = icp(q,p,10); Aligns the points of p to the points q with 10 iterations of the algorithm. The transformation is then applied using R*p + repmat(T,1,length(p)); The file has implemented both point to point and point to plane as well as a couple of other features such as extrapolation, weighting functions, edge point rejection, etc.

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. 

This plugin registers (= aligns, matches) a stack of image slices.