Alignment of slices

Depending on the image acquisition process, images of slices may be incorrectly aligned. To align the sections along a transversal axis to construct a coherent stack in three dimensions, use the Slice Alignment Tool  from the Toolbar.

In BioVis3D the alignment process is performed in an adjacent couple basis, i.e., the second slice is aligned with respect to the first one, the third one with respect to the second one, and so forth. The process of aligning two adjacent slices is called registration.  

Tip: If possible, before sectioning include at least two straight traces perpendicular to the sections, along the material of study. This makes it easy to detect points in correspondence between different slices, and simplifies the slice algnment process.

Note: if the order of slices is not correct in the sequence (for instance, slice in position 10 should be in position 23), move the slice to the right position as explained in Move Slice.

Registering a slice involves the following steps:

  1. Open the slice.

  2. Select the Slice Alignment Tool button from the Toolbar.

  3. You can change the level of transparency of the open slice in order to view the slice below it and detect misalignments.

  4. Translate or rotate the slice using the mouse or the arrow keys.

  5. You can zoom in or zoom out the slice to find an apropriate view.

See also: Overview