Dataset Registration


The detailed tutorials of all kinds of registration methods are described in Avizo User’s Guide, Chapter 13.9. This pages pick up some tips and tricks learned from the User’s Guide.

Different Registration Methods

  1. Manual alignment: Use Transformation Editor

  2. Feature alignment: Use Landmarks (2-sets), connected with “Landmark surface warp” or “Landmark Image warp”.

  3. You can retrieve the transformation from the Landmark sets by using Tcl commands in the console or in a script. In the Avizo console, type:

    >"Landmarks-2-sets" computeRigidTransform
  4. This computes a rigid transformation that moves the points of the first set as close as possible onto the points of the second set (the sum of the squared distances between corresponding points is minimized). The result is returned as a 4x4 transformation matrix, which, for example, can be used to transform some other data object using the setTransform command. For instance, type:

    >eval "" setTransform ["Landmarks-2-sets" computeRigidTransform]
  5. By default computeRigidTransform transforms the 1st landmark set into the 2nd one. You can specify which sets and order to use in the command. The command computeLinearTransform is available to compute transformations with scaling. See reference Data Type: Landmarks for more detail.

  6. Automatic alignment of fully overlaped datasets based on image comparison: Use Geometry Transform > Register Images. May down-sample before image registration to speed up the iterative algorithm. For extended options, see User’s guide pages 356-359

  7. Allow choosing partially overlapped subvolumes: Use Geometry Transforms > Image Registration Wizard

  8. Slice alignment: Geometry Transforms > Align Slices

  9. Merge aligned 3D images: Use Compute > Volume Operations > Merge