4 Registration

This stage performs registration on the normalized input. ExSequence does affine and thin plate spine registration. The registration method is presented in Murray at al 2015 in Cell. It uses a combination of 3D Harris Corner detection as well as 3D SIFT. The algorithm calculates correspondences between the reference round and the other rounds saving the results in a file:

• globalkeys_basename-downsample_round###.mat

This allows for quick access to the features for further processing. After verifying the correspondences, a Thin Plate Spine is calculated to allow for fine grained corrections in the warping. For more information on the registration step see registrations's dedicated wiki.

For each round a summedNorm directory is created containing a .mat file containing a list of keypoints which are used to warp the rounds to the reference round (chosen in the parameters file). For the reference round, symlinks are created for each color channel (appending _affine to the file name) to the files produced by the normalization step. For the other rounds new images are created which are registered to the reference round.